NM_017946.4(FKBP14):c.362dup (p.Glu122fs) AND Ehlers-Danlos syndrome, kyphoscoliotic type, 2
- Germline classification:
- Pathogenic/Likely pathogenic (13 submissions)
- Last evaluated:
- Jan 27, 2024
- Review status:
- 2 stars out of maximum of 4 starscriteria provided, multiple submitters, no conflicts
- Somatic classification
of clinical impact: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Somatic classification
of oncogenicity: - None
- Review status:
- (0/4) 0 stars out of maximum of 4 starsno assertion criteria provided
- Record status:
- current
- Accession:
- RCV000533832.29
Allele description [Variation Report for NM_017946.4(FKBP14):c.362dup (p.Glu122fs)]
NM_017946.4(FKBP14):c.362dup (p.Glu122fs)
- Genes:
- FKBP14:FKBP prolyl isomerase 14 [Gene - OMIM - HGNC]
FKBP14-AS1:FKBP14 antisense RNA 1 [Gene - HGNC] - Variant type:
- Duplication
- Cytogenetic location:
- 7p14.3
- Genomic location:
- Preferred name:
- NM_017946.4(FKBP14):c.362dup (p.Glu122fs)
- Other names:
- p.Glu122fs
- HGVS:
- NC_000007.14:g.30019115dup
- NG_032173.1:g.12691dup
- NM_017946.4:c.362dupMANE SELECT
- NP_060416.1:p.Glu122fs
- LRG_454t1:c.362dup
- LRG_454:g.12691dup
- NC_000007.13:g.30058726_30058727insG
- NC_000007.13:g.30058731dup
- NM_017946.2:c.362dupC
- NM_017946.3:c.362dupC
- NR_046478.2:n.648dup
- NR_046479.2:n.404dup
- p.Glu122Argfs*7
This HGVS expression did not pass validation- Protein change:
- E122fs
- Links:
- OMIM: 614505.0001; dbSNP: rs542489955
- NCBI 1000 Genomes Browser:
- rs542489955
- Molecular consequence:
- NM_017946.4:c.362dup - frameshift variant - [Sequence Ontology: SO:0001589]
- NR_046478.2:n.648dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- NR_046479.2:n.404dup - non-coding transcript variant - [Sequence Ontology: SO:0001619]
- Observations:
- 6
Condition(s)
Assertion and evidence details
Submission Accession | Submitter | Review Status (Assertion method) | Clinical Significance (Last evaluated) | Origin | Method | Citations |
---|---|---|---|---|---|---|
SCV000045487 | OMIM | no assertion criteria provided | Pathogenic (Feb 10, 2012) | germline | literature only | |
SCV000652309 | Labcorp Genetics (formerly Invitae), Labcorp | criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) | Pathogenic (Jan 27, 2024) | germline | clinical testing | |
SCV000929975 | GeneReviews | no classification provided | not provided | germline | literature only | |
SCV001369762 | Centre for Mendelian Genomics, University Medical Centre Ljubljana | criteria provided, single submitter (ACMG Guidelines, 2015) | Likely pathogenic (Jan 20, 2020) | unknown | clinical testing | |
SCV001429022 | Institute of Human Genetics, University of Leipzig Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 10, 2019) | germline | clinical testing | |
SCV001524457 | Baylor Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Mar 26, 2019) | paternal | clinical testing | |
SCV001593267 | Research Centre for Medical Genetics, Federal State Budgetary Scientific Institution | no assertion criteria provided | Pathogenic (Oct 23, 2020) | germline | clinical testing | |
SCV002043791 | Equipe Genetique des Anomalies du Developpement, Université de Bourgogne | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic | biparental | clinical testing | |
SCV002810392 | Fulgent Genetics, Fulgent Genetics | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Jul 22, 2021) | unknown | clinical testing | |
SCV003822048 | Revvity Omics, Revvity | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (Apr 30, 2022) | germline | clinical testing | |
SCV003924401 | Molecular Genetic Pathology Unit, University Of Rochester Medical Center | criteria provided, single submitter (ACMG Guidelines, 2015) | Pathogenic (May 16, 2023) | germline | clinical testing | |
SCV004099663 | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) | Pathogenic (Sep 8, 2023) | germline | clinical testing | |
SCV005199982 | Solve-RD Consortium | no assertion criteria provided | Likely pathogenic (Jun 1, 2022) | inherited | provider interpretation |
Summary from all submissions
Ethnicity | Origin | Affected | Individuals | Families | Chromosomes tested | Number Tested | Family history | Method |
---|---|---|---|---|---|---|---|---|
not provided | biparental | yes | not provided | 1 | not provided | not provided | not provided | clinical testing |
not provided | germline | yes | 2 | not provided | not provided | not provided | not provided | clinical testing |
not provided | germline | not provided | not provided | not provided | not provided | not provided | not provided | literature only |
not provided | germline | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing, literature only |
not provided | inherited | yes | not provided | not provided | not provided | not provided | not provided | provider interpretation |
not provided | paternal | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | yes | not provided | not provided | not provided | not provided | not provided | clinical testing |
not provided | unknown | unknown | not provided | not provided | not provided | not provided | not provided | clinical testing |
Russia | germline | not provided | 5 | 5 | not provided | not provided | not provided | clinical testing |
Citations
PubMed
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.
Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group, Topper S.
Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.
- PMID:
- 28492532
- PMCID:
- PMC5632818
Ehlers-Danlos syndrome related to FKBP14 mutations: detailed cutaneous phenotype.
Bursztejn AC, Baumann M, Lipsker D.
Clin Exp Dermatol. 2017 Jan;42(1):64-67. doi: 10.1111/ced.12983. Epub 2016 Nov 30. Review.
- PMID:
- 27905128
Details of each submission
From OMIM, SCV000045487.4
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (3) |
Description
In 5 patients with Ehlers-Danlos syndrome with progressive kyphoscoliosis, myopathy, and hearing loss (EDSKSCL2; 614557) from 4 unrelated families of Austrian, Italian, French, and Turkish origin, Baumann et al. (2012) identified homozygosity for a 1-bp duplication within a 5C-nucleotide repeat in exon 3 (c.362dupC, NM_017946.2) of the FKBP14 gene, causing a frameshift predicted to result in a premature termination codon (Glu122ArgfsTer7). Western blot analysis demonstrated absence of FKBP14 in patient fibroblasts, and qRT-PCR analysis showed strongly reduced FKBP14 expression compared to controls, consistent with nonsense-mediated decay. In an unrelated patient with EDSKMH, Baumann et al. (2012) identified compound heterozygosity for the 362dupC mutation and a 19-bp deletion (42_60del) in exon 1 of the FKBP14 gene (614505.0002), also predicted to result in a premature termination codon. The 362dupC mutation was linked to the same haplotype in all individuals, despite their geographically diverse origins, suggesting a possible founder event. Neither mutation was found in 200 controls of European descent.
In an 8-year-old Italian boy with EDSKSCL, Dordoni et al. (2016) identified compound heterozygosity for the recurrent c.362dupC mutation in exon 3 of the FKBP14 gene, and an in-frame 3-bp deletion (c.573_575del; 614505.0004) in exon 4, causing deletion of 1 residue (Glu191del). His unaffected parents were each heterozygous for 1 of the mutations.
By sequencing of genes in a targeted panel for Ehlers-Danlos syndrome, Castori et al. (2019) identified homozygosity for the recurrent c.362dupC mutation in the FKBP14 gene in a 15-year-old girl with EDSKSCL who showed severe involvement of the lower limb muscles. Her unaffected parents were heterozygous for the mutation.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Labcorp Genetics (formerly Invitae), Labcorp, SCV000652309.9
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (4) |
Description
This sequence change creates a premature translational stop signal (p.Glu122Argfs*7) in the FKBP14 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FKBP14 are known to be pathogenic (PMID: 22265013). This variant is present in population databases (rs542489955, gnomAD 0.1%), and has an allele count higher than expected for a pathogenic variant. This premature translational stop signal has been observed in individuals with Ehlers-Danlos syndrome (PMID: 22265013, 24677762, 27149304). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 279809). For these reasons, this variant has been classified as Pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From GeneReviews, SCV000929975.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | literature only | PubMed (4) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Centre for Mendelian Genomics, University Medical Centre Ljubljana, SCV001369762.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
This variant was classified as: Likely pathogenic. The following ACMG criteria were applied in classifying this variant: PS1,PM2. This variant was detected in homozygous state.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Institute of Human Genetics, University of Leipzig Medical Center, SCV001429022.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | 1 | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Baylor Genetics, SCV001524457.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (5) |
Description
This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. This variant has been previously reported in multiple affected families as disease-causing [PMID 22265013, 27905128, 28617417, 24677762]
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | paternal | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Research Centre for Medical Genetics, Federal State Budgetary Scientific Institution, SCV001593267.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | Russia | 5 | not provided | not provided | clinical testing | PubMed (2) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | not provided | not provided | not provided | not provided | 5 | not provided | 5 | not provided |
From Equipe Genetique des Anomalies du Developpement, Université de Bourgogne, SCV002043791.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (2) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | biparental | yes | not provided | Blood | not provided | not provided | not provided | 1 | not provided |
From Fulgent Genetics, Fulgent Genetics, SCV002810392.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | unknown | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Revvity Omics, Revvity, SCV003822048.2
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Molecular Genetic Pathology Unit, University Of Rochester Medical Center, SCV003924401.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | 1 | not provided | not provided | clinical testing | PubMed (5) |
Description
This variant was identified in the homozygous state in a patient with kyphoscoliotic Ehlers-Danlos Syndrome (kEDS). This frameshift variant causes a premature termination codon and is predicted to result in loss-of-function. This variant is a known pathogenic variant that has been reported multiple times in patients with kEDS, as either homozygous or compound heterozygous. This variant has been submitted to ClinVar as pathogenic over twenty times.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | yes | not provided | not provided | not provided | 1 | not provided | not provided | not provided |
From Women's Health and Genetics/Laboratory Corporation of America, LabCorp, SCV004099663.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | clinical testing | PubMed (1) |
Description
Variant summary: FKBP14 c.362dupC (p.Glu122ArgfsX7) results in a premature termination codon, predicted to cause a truncation of the encoded protein or absence of the protein due to nonsense mediated decay, which are commonly known mechanisms for disease. The variant allele was found at a frequency of 0.00055 in 207878 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in FKBP14 causing Ehlers-Danlos Syndrome, Kyphoscoliotic And Deafness Type. c.362dupC has been reported in the literature in multiple individuals affected with Ehlers-Danlos Syndrome, Kyphoscoliotic And Deafness Type (e.g., Colman_2022). These data indicate that the variant is very likely to be associated with disease. The following publication has been ascertained in the context of this evaluation (PMID: 36054293). 20 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and all submitters classified the variant as pathogenic/likely pathogenic. Based on the evidence outlined above, the variant was classified as pathogenic.
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | germline | unknown | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
From Solve-RD Consortium, SCV005199982.1
# | Ethnicity | Individuals | Chromosomes Tested | Family History | Method | Citations |
---|---|---|---|---|---|---|
1 | not provided | not provided | not provided | not provided | provider interpretation | not provided |
Description
Variant confirmed as disease-causing by referring clinical team
# | Sample | Method | Observation | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Origin | Affected | Number tested | Tissue | Purpose | Method | Individuals | Allele frequency | Families | Co-occurrences | |
1 | inherited | yes | not provided | not provided | not provided | not provided | not provided | not provided | not provided |
Last Updated: Nov 24, 2024