VCV001708456.4 - ClinVar

NM_001312909.2(FAM111A):c.364C>T (p.Gln122Ter)

Germline

Classification

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.

(3)

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.

Conflicting classifications of pathogenicity
Pathogenic(1); Uncertain significance(2)

criteria provided, conflicting classifications

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_001312909.2(FAM111A):c.364C>T (p.Gln122Ter)

Variation ID: 1708456 Accession: VCV001708456.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 11q12.1 11: 59152032 (GRCh38) [ NCBI UCSC ] 11: 58919505 (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	Oct 8, 2022	Jul 7, 2024	Jan 22, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_001312909.2:c.364C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001299838.1:p.Gln122Ter	nonsense
NM_001142519.3:c.364C>T	NP_001135991.1:p.Gln122Ter	nonsense
NM_001142520.3:c.364C>T	NP_001135992.1:p.Gln122Ter	nonsense
NM_001142521.3:c.364C>T	NP_001135993.1:p.Gln122Ter	nonsense
NM_001312910.2:c.364C>T	NP_001299839.1:p.Gln122Ter	nonsense
NM_001312911.2:c.364C>T	NP_001299840.1:p.Gln122Ter	nonsense
NM_001369457.1:c.364C>T	NP_001356386.1:p.Gln122Ter	nonsense
NM_001374804.1:c.364C>T	NP_001361733.1:p.Gln122Ter	nonsense
NM_001374848.1:c.364C>T	NP_001361777.1:p.Gln122Ter	nonsense
NM_001374849.1:c.364C>T	NP_001361778.1:p.Gln122Ter	nonsense
NM_001374850.1:c.364C>T	NP_001361779.1:p.Gln122Ter	nonsense
NM_001374851.1:c.364C>T	NP_001361780.1:p.Gln122Ter	nonsense
NM_001374852.1:c.364C>T	NP_001361781.1:p.Gln122Ter	nonsense
NM_001374853.1:c.364C>T	NP_001361782.1:p.Gln122Ter	nonsense
NM_001374854.1:c.364C>T	NP_001361783.1:p.Gln122Ter	nonsense
NM_001374855.1:c.364C>T	NP_001361784.1:p.Gln122Ter	nonsense
NM_001374856.1:c.364C>T	NP_001361785.1:p.Gln122Ter	nonsense
NM_001374857.1:c.364C>T	NP_001361786.1:p.Gln122Ter	nonsense
NM_001374858.1:c.364C>T	NP_001361787.1:p.Gln122Ter	nonsense
NM_001374859.1:c.364C>T	NP_001361788.1:p.Gln122Ter	nonsense
NM_001374860.1:c.364C>T	NP_001361789.1:p.Gln122Ter	nonsense
NM_001374861.1:c.364C>T	NP_001361790.1:p.Gln122Ter	nonsense
NM_001374862.1:c.364C>T	NP_001361791.1:p.Gln122Ter	nonsense
NM_001374863.1:c.364C>T	NP_001361792.1:p.Gln122Ter	nonsense
NM_001374864.1:c.364C>T	NP_001361793.1:p.Gln122Ter	nonsense
NM_001374865.1:c.364C>T	NP_001361794.1:p.Gln122Ter	nonsense
NM_001374866.1:c.364C>T	NP_001361795.1:p.Gln122Ter	nonsense
NM_001374867.1:c.364C>T	NP_001361796.1:p.Gln122Ter	nonsense
NM_001374868.1:c.364C>T	NP_001361797.1:p.Gln122Ter	nonsense
NM_001374869.1:c.364C>T	NP_001361798.1:p.Gln122Ter	nonsense
NM_001374870.1:c.364C>T	NP_001361799.1:p.Gln122Ter	nonsense
NM_022074.3:c.364C>T
NM_022074.4:c.364C>T	NP_071357.2:p.Gln122Ter	nonsense
NM_198847.3:c.364C>T	NP_942144.1:p.Gln122Ter	nonsense
NC_000011.10:g.59152032C>T
NC_000011.9:g.58919505C>T
NG_042835.1:g.14287C>T

... more HGVS ... less HGVS

Protein change

Q122*

Other names

Canonical SPDI

NC_000011.10:59152031:C:T

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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

VarSome

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
Gene	OMIM	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.
FAM111A		-	-	GRCh38 GRCh37	240	266

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.
FAM111A-related disorder	Uncertain significance (1)	criteria provided, single submitter	Nov 21, 2022	RCV003408213.4
not provided	Uncertain significance (1)	criteria provided, single submitter	Jan 22, 2024	RCV003738179.2
See cases	Pathogenic (1)	criteria provided, single submitter	Dec 15, 2021	RCV004584564.1

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.
Uncertain significance (Nov 21, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	FAM111A-related condition Affected status: unknown Allele origin: germline	PreventionGenetics, part of Exact Sciences Accession: SCV004107039.1 First in ClinVar: Nov 20, 2023 Last updated: Nov 20, 2023	Comment: The FAM111A c.364C>T variant is predicted to result in premature protein termination (p.Gln122). To our knowledge, this variant has not been reported in the literature. … (more) The FAM111A c.364C>T variant is predicted to result in premature protein termination (p.Gln122). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0039% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-58919505-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. (less)
Uncertain significance (Jan 22, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	not provided Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV004553490.1 First in ClinVar: Feb 20, 2024 Last updated: Feb 20, 2024	Comment: This sequence change creates a premature translational stop signal (p.Gln122) in the FAM111A gene. While this is not anticipated to result in nonsense mediated decay, … (more) This sequence change creates a premature translational stop signal (p.Gln122) in the FAM111A gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 490 amino acid(s) of the FAM111A protein. This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with FAM111A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1708456). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. (less)
Pathogenic (Dec 15, 2021)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	see cases Affected status: yes Allele origin: unknown	Institute of Human Genetics, University Hospital Muenster Accession: SCV002578104.2 First in ClinVar: Oct 08, 2022 Last updated: Jul 07, 2024	Comment: ACMG categories: PVS1,PM2,PP3 Number of individuals with the variant: 1 Clinical Features: Short stature (present) Age: 10-19 years Sex: male Tissue: blood

Comment:

The FAM111A c.364C>T variant is predicted to result in premature protein termination (p.Gln122*). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0039% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/11-58919505-C-T). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

Comment:

This sequence change creates a premature translational stop signal (p.Gln122*) in the FAM111A gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 490 amino acid(s) of the FAM111A protein. This variant is present in population databases (no rsID available, gnomAD 0.004%). This variant has not been reported in the literature in individuals affected with FAM111A-related conditions. ClinVar contains an entry for this variant (Variation ID: 1708456). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

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.

Comment:

Citations for germline classification of this variant

There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar.

Text-mined citations for this variant ...

Record last updated Nov 25, 2024

ClinVar Genomic variation as it relates to human health

NM_001312909.2(FAM111A):c.364C>T (p.Gln122Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...