ClinVar Genomic variation as it relates to human health
NM_001025295.3(IFITM5):c.-14C>T
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
-
NM_001025295.3(IFITM5):c.-14C>T
Variation ID: 37143 Accession: VCV000037143.48
- Type and length
-
single nucleotide variant, 1 bp
- Location
-
Cytogenetic: 11p15.5 11: 299504 (GRCh38) [ NCBI UCSC ] 11: 299504 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
-
First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Mar 24, 2015 Oct 20, 2024 Jan 10, 2024 - HGVS
-
Nucleotide Protein Molecular
consequenceNM_001025295.3:c.-14C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
5 prime UTR NC_000011.10:g.299504G>A NC_000011.9:g.299504G>A NG_032892.1:g.5023C>T - Protein change
- -
- Other names
-
-14C-T, 5-PRIME UTR
- Canonical SPDI
- NC_000011.10:299503:G:A
-
Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
-
Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
- -
-
Allele frequency
Help
The frequency of the allele represented by this VCV record.
- -
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
---|---|---|---|---|---|---|
HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
|||
IFITM5 | - | - |
GRCh38 GRCh37 |
132 | 179 | |
PGGHG | - | - |
GRCh38 GRCh37 |
10 | 49 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
---|---|---|---|---|
Pathogenic (11) |
criteria provided, multiple submitters, no conflicts
|
Dec 1, 2023 | RCV000030773.23 | |
Pathogenic (5) |
criteria provided, multiple submitters, no conflicts
|
Jan 10, 2024 | RCV001269708.30 | |
Pathogenic (1) |
criteria provided, single submitter
|
Jun 14, 2021 | RCV001526510.3 | |
Pathogenic (2) |
criteria provided, multiple submitters, no conflicts
|
Feb 21, 2023 | RCV002277112.6 | |
IFITM5-related disorder
|
Pathogenic (1) |
no assertion criteria provided
|
Sep 2, 2024 | RCV004757954.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
|
---|---|---|---|---|---|
Pathogenic
(May 28, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
Affected status: unknown
Allele origin:
unknown
|
Mendelics
Accession: SCV001138196.1
First in ClinVar: Jan 08, 2020 Last updated: Jan 08, 2020 |
|
|
Pathogenic
(Jun 14, 2021)
|
criteria provided, single submitter
Method: not provided
|
Osteoporosis
Affected status: yes
Allele origin:
germline
|
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin
Additional submitter:
CUBI - Core Unit Bioinformatics, Berlin Institute of Health
Accession: SCV001736930.1
First in ClinVar: Jun 19, 2021 Last updated: Jun 19, 2021 |
Clinical Features:
Increased susceptibility to fractures (present) , Hyperplastic callus formation (present) , Short stature (present)
Sex: male
Tissue: Blood
|
|
Pathogenic
(Jun 02, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV004020761.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
Comment:
Variant summary: IFITM5 c.-14C>T is located in the untranslated mRNA region upstream of the initiation codon. It has been found to generate an upstream start … (more)
Variant summary: IFITM5 c.-14C>T is located in the untranslated mRNA region upstream of the initiation codon. It has been found to generate an upstream start codon which results in an IFITM5 protein with five additional amino acids at its N-terminus (Cho_2012). The variant was absent in 72430 control chromosomes (gnomAD). c.-14C>T has been reported in the literature in the heterozygous state in multiple individuals affected with Osteogenesis Imperfecta Type 5, has been found to segregate with the disease phenotype in multiple families, and has been reported as a de novo occurrence in several affected individuals (e.g. Cho_2012, Liu_2017). These data indicate that the variant is very likely to be associated with disease. The following publications have been ascertained in the context of this evaluation (PMID: 22863190, 28725987). Fourteen submitters have provided clinical-significance assessments for this variant to ClinVar after 2014 and all classified the variant as pathogenic (n=13)/likely pathogenic (n=1). Based on the evidence outlined above, the variant was classified as pathogenic. (less)
|
|
Pathogenic
(Jun 30, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
Affected status: unknown
Allele origin:
unknown
|
Illumina Laboratory Services, Illumina
Accession: SCV004101347.1
First in ClinVar: Nov 11, 2023 Last updated: Nov 11, 2023 |
Comment:
The IFITM5 c.-14C>T variant occurs in the 5' untranslated region. Across a selection of the available literature, this variant has been identified in over 95 … (more)
The IFITM5 c.-14C>T variant occurs in the 5' untranslated region. Across a selection of the available literature, this variant has been identified in over 95 individuals with variable phenotypes consistent with osteogenesis imperfecta, type V (PMID: 22863190; 23240094; 23408678; 23612438; 23674381; 23813632; 24674092; 31159867; 31244780). Both familial segregation as well as de novo occurrences have been observed. This variant is predicted to introduce five amino acid residues at the N-terminus of the IFITM5 protein due to the creation of an in-frame translation initiation codon upstream of the wild-type initiation codon. In vitro expression of this variant in a cell line confirmed this prediction due to the presence of a slightly larger protein detected by immunoblotting (PMID: 22863190). Additionally, transgenic mice that express this variant exhibited bone abnormalities consistent with those observed in patients (PMID: 25251575). This variant has been classified as pathogenic by at least three submitters in ClinVar. This variant is not observed in version 2.1.1 or version 3.1.2 of the Genome Aggregation Database. Based on the available evidence, the c.-14C>T variant is classified as pathogenic for osteogenesis imperfecta, type V. (less)
|
|
Pathogenic
(Jan 10, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV002234738.3
First in ClinVar: Mar 28, 2022 Last updated: Feb 14, 2024 |
Comment:
This variant occurs in a non-coding region of the IFITM5 gene. It does not change the encoded amino acid sequence of the IFITM5 protein. This … (more)
This variant occurs in a non-coding region of the IFITM5 gene. It does not change the encoded amino acid sequence of the IFITM5 protein. This variant is not present in population databases (gnomAD no frequency). This variant has been observed in individual(s) with osteogenesis imperfecta (PMID: 22863190, 23977282, 31099171). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 37143). For these reasons, this variant has been classified as Pathogenic. (less)
|
|
Pathogenic
(Sep 25, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
Affected status: unknown
Allele origin:
germline
|
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories
Accession: SCV004562575.1
First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024 |
Comment:
The IFITM5 c.-14C>T variant (rs587776916) is reported in the literature as a recurrent variant in individuals affected with osteogenesis imperfecta type V, including several de … (more)
The IFITM5 c.-14C>T variant (rs587776916) is reported in the literature as a recurrent variant in individuals affected with osteogenesis imperfecta type V, including several de novo occurrences (Cho 2012, Lazarus 2014, Maddirevula 2018, Rauch 2013, Shapiro 2013, Tyurin 2022, Zhytnik 2019). This variant is also reported in ClinVar (Variation ID: 37143), but is absent from the Genome Aggregation Database, indicating it is not a common polymorphism. This variant is located in the 5' untranslated region and creates a novel protein translation start codon, resulting in the addition of five amino acids (Cho 2012, Lazarus 2014). Based on available information, this variant is considered to be pathogenic. References: Cho TJ et al. A single recurrent mutation in the 5'-UTR of IFITM5 causes osteogenesis imperfecta type V. Am J Hum Genet. 2012 Aug 10;91(2):343-8. PMID: 22863190. Lazarus S et al. The IFITM5 mutation c.-14C > T results in an elongated transcript expressed in human bone; and causes varying phenotypic severity of osteogenesis imperfecta type V. BMC Musculoskelet Disord. 2014 Mar 27;15:107. PMID: 24674092. Maddirevula S et al. Expanding the phenome and variome of skeletal dysplasia. Genet Med. 2018 Dec;20(12):1609-1616. PMID: 29620724. Rauch F et al. Osteogenesis imperfecta type V: marked phenotypic variability despite the presence of the IFITM5 c.-14C>T mutation in all patients. J Med Genet. 2013 Jan;50(1):21-4. PMID: 23240094. Shapiro JR et al. Phenotypic variability of osteogenesis imperfecta type V caused by an IFITM5 mutation. J Bone Miner Res. 2013 Jul;28(7):1523-30. PMID: 23408678. Tyurin A et al. Does the c.-14C>T Mutation in the IFITM5 Gene Provide Identical Phenotypes for Osteogenesis Imperfecta Type V? Data from Russia and a Literature Review. Biomedicines. 2022 Sep 22;10(10):2363. PMID: 36289625. Zhytnik L et al. IFITM5 pathogenic variant causes osteogenesis imperfecta V with various phenotype severity in Ukrainian and Vietnamese patients. Hum Genomics. 2019 Jun 3;13(1):25. PMID: 31159867. (less)
|
|
Pathogenic
(Nov 30, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Not provided
Affected status: yes
Allele origin:
germline
|
Blueprint Genetics
Accession: SCV001832283.1
First in ClinVar: Sep 08, 2021 Last updated: Sep 08, 2021
Comment:
Patient analyzed with Comprehensive Skeletal Dysplasias and Disorders Panel
|
|
|
Pathogenic
(-)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
de novo
|
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India
Accession: SCV002054003.1
First in ClinVar: Jan 08, 2022 Last updated: Jan 08, 2022 |
|
|
Pathogenic
(Sep 07, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta
Affected status: unknown
Allele origin:
germline
|
Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV002564848.1
First in ClinVar: Aug 29, 2022 Last updated: Aug 29, 2022 |
|
|
Pathogenic
(Feb 21, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
Accession: SCV003804269.1
First in ClinVar: Feb 25, 2023 Last updated: Feb 25, 2023 |
Clinical Features:
Increased susceptibility to fractures (present) , Elevated alkaline phosphatase of bone origin (present)
|
|
Pathogenic
(Nov 17, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV002028039.2
First in ClinVar: Nov 29, 2021 Last updated: Mar 04, 2023 |
Comment:
Published functional studies in mice demonstrate that c.-14 C>T results in severe skeletal defects caused by alterations to protein interactions and signaling cascades that affect … (more)
Published functional studies in mice demonstrate that c.-14 C>T results in severe skeletal defects caused by alterations to protein interactions and signaling cascades that affect differentiation and mineralization of bone (Lietman et al., 2015); Not observed in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 23674381, 31715670, 24674092, 23612438, 23408678, 23240094, 23977282, 27678411, 27029692, 25251575, 22863190, 22863195, 24478195, 29499418, 29188603, 29620724, 31159867, 31244780, 31099171, 32552793, 32770541, 33470886, 33935965, 32123938, 33939306, 33726816, 33360005) (less)
|
|
Pathogenic
(Dec 01, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
Affected status: yes
Allele origin:
germline
|
Laboratory of Medical Genetics, National & Kapodistrian University of Athens
Accession: SCV005091050.1
First in ClinVar: Aug 04, 2024 Last updated: Aug 04, 2024 |
Comment:
PS3, PS4, PM2, PP5 - Well-established functional studies show damaging effect on the gene or gene product. Low frequency in gnomAD population databases. This variant … (more)
PS3, PS4, PM2, PP5 - Well-established functional studies show damaging effect on the gene or gene product. Low frequency in gnomAD population databases. This variant has been previously reported as causative for Osteogenesis imperfecta. (PMID:38681748). (less)
|
|
Pathogenic
(Jun 19, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics
Accession: SCV000928325.1
First in ClinVar: Aug 31, 2019 Last updated: Aug 31, 2019 |
Comment:
Heterozygous variant c.-14C>T in 5' UTR has been observed in IFITM5 gene. The proband born of a non-consanguineous marriage, presented with clinical indications of inability … (more)
Heterozygous variant c.-14C>T in 5' UTR has been observed in IFITM5 gene. The proband born of a non-consanguineous marriage, presented with clinical indications of inability to stand or walk, traumatic fracture in midshaft of the right femur and had soft skull at birth. X-ray showed multiple rib fractures. The patient in our clinical analysis was diagnosed with the said variant in an autosomal dominant mode of inheritance. This variant introduces alternative start codon, adding 5 amino acid residues to the N terminus of the protein. Transgenic mice models show that mutant IFITM5 mice exhibit perinatal lethality with severe defects of the long bones and ribs (Lietman CD et al. Journal of Bone and Mineral Research 2015). The variant has not been reported in the 1000 genomes and ExAC databases and has a minor allele frequency of 0.02%. The in silico prediction of the variant is possibly damaging by MutationTaster2. In summary, the said variant meets our criteria to be classified as pathogenic based on the mode of inheritance, in silico prediction and allele frequency in population databases. (less)
Clinical Features:
Inability to walk (present) , Pathologic fracture (present)
Age: 0-9 years
Sex: male
Ethnicity/Population group: Indian Hindu
Geographic origin: India
Method: DNA was used to perform targeted gene sequencing using a custom capture kit. Libraries were sequenced to mean >80-100X coverage in Illumina sequencing platform. Sequence obtained were aligned to a human reference genome using BWA program and analyzed using Picard and GATK-Lite toolkit to identify variants in the targeted genes relevant to clinical indication.
|
|
Pathogenic
(Sep 26, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
Clinical Genetics and Genomics, Karolinska University Hospital
Accession: SCV001449901.1
First in ClinVar: Dec 11, 2020 Last updated: Dec 11, 2020 |
Number of individuals with the variant: 1
|
|
Pathogenic
(Apr 20, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
Affected status: yes
Allele origin:
germline
|
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein
Accession: SCV002512270.1
First in ClinVar: May 21, 2022 Last updated: May 21, 2022 |
Comment:
ACMG classification criteria: PS3 supporting, PS4, PM2, PM6 strong, PP1
Geographic origin: Brazil
|
|
Pathogenic
(Jul 17, 2023)
|
criteria provided, single submitter
Method: clinical testing
|
Osteogenesis imperfecta type 5
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute
Additional submitter:
Shariant Australia, Australian Genomics
Accession: SCV002767906.2
First in ClinVar: Dec 24, 2022 Last updated: Jul 23, 2024 |
Comment:
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Neomorphic gain of function is the proposed … (more)
Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0101 - Neomorphic gain of function is the proposed mechanism of disease in this gene and is associated with osteogenesis imperfecta, type V (MIM# 610967) (PMID: 35216266). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0217 - Non-coding variant shown to affect the translated protein. This variant introduces an alternative in-frame translation start site upstream, resulting in 5 additional amino acids at the N-terminus (PMIDs: 22863190, 22863195). (SP) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0801 - This variant has strong previous evidence of pathogenicity in unrelated individuals. It has been reported in more than 15 unrelated patients with osteogenesis imperfecta type V (ClinVar; PMIDs: 22863190, 22863195, 31159867). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Knockin mice embryos with this variant revealed skeletal anomalies (PMID: 29174564). In addition, when overexpressed in MC3T3-E1 and MLO-A5 cells, this variant activated the reporters dependent on MEF2, NFATc, and NR4A significantly compared to wild type (PMID: 35216266). (SP) 1204 - This variant has been shown to be de novo in the proband (parental status not tested but assumed) (by segregation analysis). (SP) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign (less)
|
|
Pathogenic
(Mar 01, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV001746970.20
First in ClinVar: Jul 10, 2021 Last updated: Oct 20, 2024 |
Number of individuals with the variant: 1
|
|
Likely pathogenic
(Jun 18, 2018)
|
no assertion criteria provided
Method: clinical testing
|
Osteogenesis imperfecta type 5
Affected status: yes
Allele origin:
germline
|
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare
Accession: SCV000863906.1
First in ClinVar: Dec 24, 2018 Last updated: Dec 24, 2018 |
|
|
Pathogenic
(Mar 01, 2015)
|
no assertion criteria provided
Method: literature only
|
OSTEOGENESIS IMPERFECTA, TYPE V
Affected status: not provided
Allele origin:
germline
|
OMIM
Accession: SCV000053434.5
First in ClinVar: Apr 04, 2013 Last updated: Apr 23, 2022 |
Comment on evidence:
In 19 Korean individuals (13 from 3 families and 6 simplex individuals) with osteogenesis imperfecta type V (OI5; 610967), Cho et al. (2012) identified a … (more)
In 19 Korean individuals (13 from 3 families and 6 simplex individuals) with osteogenesis imperfecta type V (OI5; 610967), Cho et al. (2012) identified a C-T transition 5-prime UTR of the IFITM5 gene (-14C-T). Semler et al. (2012) identified the same mutation in 2 unrelated individuals with OI5. The mutation was predicted to generate an in-frame translation start codon that would add 5 amino acids (Met-Ala-Leu-Glu-Pro) to the N terminus of IFITM5, which was confirmed in transfection experiments. Rauch et al. (2013) sequenced exon 1 of the IFITM5 gene in 42 patients with OI5 from 23 different families and identified the c.-14C-T mutation in all. The authors noted that despite the presence of the same mutation, the patients exhibited marked interindividual phenotypic variability. In 17 affected individuals from 12 families with OI5, Shapiro et al. (2013) identified heterozygosity for the c.-14C-T mutation in the IFITM5 gene. The authors noted strikingly variable phenotypic expressivity, both within and between affected OI5 families. In a 5.5-year-old Hispanic girl with OI, Grover et al. (2013) identified heterozygosity for a de novo c.-14C-T mutation in IFITM5 that was not present in her unaffected parents. The patient did not exhibit any of the classic features of OI type V described in previous patients with this mutation, including hyperplastic callus formation, calcification of interosseous membranes, or radial head dislocation. In 9 patients from 8 families with OI5, Lazarus et al. (2014) identified heterozygosity for the c.-14C-T mutation. The mutation occurred de novo in the 3 simplex cases for whom parental DNA was available. All 9 patients exhibited classic features of OI5 but varied markedly in terms of bone fragility, with 1 adult patient having no history of clinical fracture. IFITM5 expression analysis in a bone sample from a 14-year-old female patient confirmed the presence of both wildtype and mutant transcripts. Lazarus et al. (2014) noted that all 95 reported OI5 patients who had been investigated for this mutation had been found to be heterozygous for it. In a 30-year-old woman of Lithuanian origin with a history of multiple fractures in childhood, who had short stature due to progressively severe skeletal deformities and loss of mobility, Guillen-Navarro et al. (2014) identified heterozygosity for the c.-14C-T mutation in IFITM5. Radiologic examination revealed some of the typical clinical features of OI5, including fracture-related hyperplastic callus formation and calcification of the interosseous membrane of the forearm; however, dislocation of the radial head and radiodense metaphysical banding were not detected. Lietman et al. (2015) generated transgenic mice with the variant corresponding to the human mutation c.-14C-T and observed perinatal lethality. Skeletal preparations and radiographs of embryonic day (E) 15.5 and E18.5 transgenic embryos revealed delayed/abnormal mineralization and skeletal defects, including abnormal rib cage formation, long bone deformities, and fractures. Primary osteoblast cultures derived from mutant calvaria at E18.5 showed decreased mineralization and reduced expression of osteoblast differentiation markers, such as osteocalcin (OC; 112260), compared to wildtype. Overexpression of wildtype Ifitm5 did not, however, manifest a significant bone phenotype. Noting that previous studies had shown that knockout of Ifitm5 did not result in significant bone abnormalities, Lietman et al. (2015) concluded that the c.-14C-T mutation acts in a neomorphic fashion. (less)
|
|
Pathogenic
(Sep 02, 2024)
|
no assertion criteria provided
Method: clinical testing
|
IFITM5-related condition
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV005356866.1
First in ClinVar: Oct 08, 2024 Last updated: Oct 08, 2024 |
Comment:
The IFITM5 c.-14C>T variant is located in the 5' untranslated region. This variant is in the 5’ untranslated region (5’UTR) of the gene and is … (more)
The IFITM5 c.-14C>T variant is located in the 5' untranslated region. This variant is in the 5’ untranslated region (5’UTR) of the gene and is a known recurrent pathogenic variant in patients with osteogenesis imperfecta (Cho et al. 2012. PubMed ID: 22863190; Lazarus et al. 2014. PubMed ID: 24674092; Mrosk et al. 2018. PubMed ID: 29499418). Functional studies have shown that this variant introduces a novel in frame start codon in the 5’UTR of the gene and results in a longer protein (Lazarus et al. 2014. PubMed ID: 24674092). This variant has not been reported in a large population database, indicating this variant is rare. This variant is interpreted as pathogenic. (less)
|
|
click to load more click to collapse |
Germline Functional Evidence
There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Citations for germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
---|---|---|---|---|
The Osteogenesis Imperfecta Type V Mutant BRIL/IFITM5 Promotes Transcriptional Activation of MEF2, NFATc, and NR4A in Osteoblasts. | Maranda V | International journal of molecular sciences | 2022 | PMID: 35216266 |
A novel variant of the IFITM5 gene within the 5'-UTR causes neonatal transverse clavicular fracture: Expanding the genetic spectrum. | Wu D | Molecular genetics & genomic medicine | 2020 | PMID: 32383316 |
IFITM5 pathogenic variant causes osteogenesis imperfecta V with various phenotype severity in Ukrainian and Vietnamese patients. | Zhytnik L | Human genomics | 2019 | PMID: 31159867 |
Expanding the phenotypic spectrum of osteogenesis imperfecta type V including heterotopic ossification of muscle origins and attachments. | Clewemar P | Molecular genetics & genomic medicine | 2019 | PMID: 31099171 |
Crispr-Cas9 engineered osteogenesis imperfecta type V leads to severe skeletal deformities and perinatal lethality in mice. | Rauch F | Bone | 2018 | PMID: 29174564 |
Gene mutation spectrum and genotype-phenotype correlation in a cohort of Chinese osteogenesis imperfecta patients revealed by targeted next generation sequencing. | Liu Y | Osteoporosis international : a journal established as result of cooperation between the European Foundation for Osteoporosis and the National Osteoporosis Foundation of the USA | 2017 | PMID: 28725987 |
A transgenic mouse model of OI type V supports a neomorphic mechanism of the IFITM5 mutation. | Lietman CD | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 2015 | PMID: 25251575 |
The IFITM5 mutation c.-14C > T results in an elongated transcript expressed in human bone; and causes varying phenotypic severity of osteogenesis imperfecta type V. | Lazarus S | BMC musculoskeletal disorders | 2014 | PMID: 24674092 |
Two mutations in IFITM5 causing distinct forms of osteogenesis imperfecta. | Guillén-Navarro E | American journal of medical genetics. Part A | 2014 | PMID: 24478195 |
Phenotype and genotype analysis of Chinese patients with osteogenesis imperfecta type V. | Zhang Z | PloS one | 2013 | PMID: 23977282 |
Osteogenesis imperfecta without features of type V caused by a mutation in the IFITM5 gene. | Grover M | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 2013 | PMID: 23674381 |
Phenotypic variability of osteogenesis imperfecta type V caused by an IFITM5 mutation. | Shapiro JR | Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research | 2013 | PMID: 23408678 |
Osteogenesis imperfecta type V: marked phenotypic variability despite the presence of the IFITM5 c.-14C>T mutation in all patients. | Rauch F | Journal of medical genetics | 2013 | PMID: 23240094 |
A mutation in the 5'-UTR of IFITM5 creates an in-frame start codon and causes autosomal-dominant osteogenesis imperfecta type V with hyperplastic callus. | Semler O | American journal of human genetics | 2012 | PMID: 22863195 |
A single recurrent mutation in the 5'-UTR of IFITM5 causes osteogenesis imperfecta type V. | Cho TJ | American journal of human genetics | 2012 | PMID: 22863190 |
click to load more click to collapse |
Text-mined citations for rs587776916 ...
HelpRecord last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.