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NM_032119.4(ADGRV1):c.3974C>T (p.Thr1325Met)

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Interpretation:
Conflicting interpretations of pathogenicity​

Likely pathogenic(1);Uncertain significance(4)

Review status:
criteria provided, conflicting interpretations
Submissions:
5 (Most recent: Aug 17, 2021)
Last evaluated:
Apr 12, 2021
Accession:
VCV000546975.14
Variation ID:
546975
Description:
single nucleotide variant
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NM_032119.4(ADGRV1):c.3974C>T (p.Thr1325Met)

Allele ID
537464
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
5q14.3
Genomic location
5: 90653548 (GRCh38) GRCh38 UCSC
5: 89949365 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000005.10:g.90653548C>T
NC_000005.9:g.89949365C>T
NG_007083.2:g.129205C>T
... more HGVS
Protein change
T1325M
Other names
-
Canonical SPDI
NC_000005.10:90653547:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
Exome Aggregation Consortium (ExAC) 0.00006
Trans-Omics for Precision Medicine (TOPMed) 0.00004
The Genome Aggregation Database (gnomAD), exomes 0.00004
The Genome Aggregation Database (gnomAD) 0.00010
Links
dbSNP: rs756414393
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Uncertain significance 2 criteria provided, multiple submitters, no conflicts Sep 12, 2020 RCV000659018.6
Uncertain significance 1 criteria provided, single submitter Oct 31, 2018 RCV000764616.1
Uncertain significance 1 criteria provided, single submitter Apr 27, 2017 RCV001155124.1
Likely pathogenic 1 criteria provided, single submitter Apr 12, 2021 RCV001375131.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
ADGRV1 - - GRCh38
GRCh37
2418 2449

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Uncertain significance
(Oct 31, 2018)
criteria provided, single submitter
Method: clinical testing
Febrile seizures, familial, 4
Usher syndrome, type 2C
Allele origin: unknown
Fulgent Genetics,Fulgent Genetics
Accession: SCV000895723.1
Submitted: (Nov 14, 2018)
Evidence details
Publications
PubMed (1)
DOI: 10.1038/gim.2015.30
Uncertain significance
(Apr 27, 2017)
criteria provided, single submitter
Method: clinical testing
Usher syndrome, type 2C
Allele origin: germline
Illumina Clinical Services Laboratory,Illumina
Accession: SCV001316533.1
Submitted: (Feb 20, 2020)
Evidence details
Publications
PubMed (1)
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
Uncertain significance
(Sep 12, 2020)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
Invitae
Accession: SCV001202716.2
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (1)
Comment:
This sequence change replaces threonine with methionine at codon 1325 of the ADGRV1 protein (p.Thr1325Met). The threonine residue is highly conserved and there is a … (more)
Uncertain significance
(Jul 01, 2018)
criteria provided, single submitter
Method: clinical testing
not provided
Allele origin: germline
CeGaT Praxis fuer Humangenetik Tuebingen
Accession: SCV000780821.9
Submitted: (Jul 04, 2021)
Evidence details
Likely pathogenic
(Apr 12, 2021)
criteria provided, single submitter
Method: clinical testing
Abnormal activity of mitochondrial respiratory chain
Allele origin: germline
Department of Otolaryngology – Head & Neck Surgery, Cochlear Implant Center
Accession: SCV001572092.2
Submitted: (Aug 17, 2021)
Evidence details
Publications
PubMed (1)
Comment:
PS1_Strong, PM2_Moderate, PP3_Supporting

Functional evidence

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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 this variant

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Title Author Journal Year Link
Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. Richards S Genetics in medicine : official journal of the American College of Medical Genetics 2015 PMID: 25741868
Screening for single nucleotide variants, small indels and exon deletions with a next-generation sequencing based gene panel approach for Usher syndrome. Krawitz PM Molecular genetics & genomic medicine 2014 PMID: 25333064

Text-mined citations for rs756414393...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 30, 2021