NM_032119.4(ADGRV1):c.14972+1G>T AND not provided

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Dec 19, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002550229.3

Allele description [Variation Report for NM_032119.4(ADGRV1):c.14972+1G>T]

NM_032119.4(ADGRV1):c.14972+1G>T

Gene:

ADGRV1:adhesion G protein-coupled receptor V1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

5q14.3

Genomic location:

Preferred name:

NM_032119.4(ADGRV1):c.14972+1G>T

HGVS:

NC_000005.10:g.90807738G>T
NG_007083.2:g.283395G>T
NM_032119.4:c.14972+1G>TMANE SELECT
LRG_1095t1:c.14972+1G>T
LRG_1095:g.283395G>T
NC_000005.9:g.90103555G>T
NM_032119.3:c.14972+1G>T

Links:

dbSNP: rs780011571

NCBI 1000 Genomes Browser:

rs780011571

Molecular consequence:

NM_032119.4:c.14972+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003299477	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely pathogenic (Dec 19, 2023)	germline	clinical testing	PubMed (9) [See all records that cite these PMIDs] 16199547, 19357117, 22135276, 22147658, 26226137, 30718709, 31047384, 32467589, 28492532
SCV004022845	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Likely pathogenic (Jul 25, 2023)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003299477

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely pathogenic
(Dec 19, 2023)

germline

clinical testing

PubMed (9)
[See all records that cite these PMIDs]

SCV004022845

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Likely pathogenic
(Jul 25, 2023)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]

PMID:: 16199547
PMCID:: PMC1735933

GPR98 mutations cause Usher syndrome type 2 in males.

Ebermann I, Wiesen MH, Zrenner E, Lopez I, Pigeon R, Kohl S, Löwenheim H, Koenekoop RK, Bolz HJ.

J Med Genet. 2009 Apr;46(4):277-80. doi: 10.1136/jmg.2008.059626.

PubMed [citation]

PMID:: 19357117

See all PubMed Citations (9)

Details of each submission

From Invitae, SCV003299477.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (9)

Description

This sequence change affects a donor splice site in intron 73 of the ADGRV1 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in ADGRV1 are known to be pathogenic (PMID: 19357117, 22135276, 22147658, 26226137, 30718709, 31047384, 32467589). This variant is present in population databases (rs780011571, gnomAD 0.002%). Disruption of this splice site has been observed in individual(s) with retinitis pigmentosa (Invitae). ClinVar contains an entry for this variant (Variation ID: 1065641). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely 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 GeneDx, SCV004022845.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

Description

Canonical splice site variant predicted to result in a null allele in a gene for which loss-of-function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); Observed with a pathogenic variant on the opposite allele (in trans) in a patient with bilateral sensorineural hearing loss referred for genetic testing at GeneDx; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 31964843)

#	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		not provided	not provided	not provided	not provided

Last Updated: Feb 28, 2024

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