NM_001692.4(ATP6V1B1):c.273+2T>A AND ATP6V1B1-related disorder

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Jun 4, 2023
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV003408066.4

Allele description [Variation Report for NM_001692.4(ATP6V1B1):c.273+2T>A]

NM_001692.4(ATP6V1B1):c.273+2T>A

Gene:

ATP6V1B1:ATPase H+ transporting V1 subunit B1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2p13.3

Genomic location:

Preferred name:

NM_001692.4(ATP6V1B1):c.273+2T>A

HGVS:

NC_000002.12:g.70958146T>A
NG_008016.1:g.27279T>A
NM_001692.4:c.273+2T>AMANE SELECT
LRG_1176t1:c.273+2T>A
LRG_1176:g.27279T>A
NC_000002.11:g.71185276T>A
NM_001692.3:c.273+2T>A

Links:

dbSNP: rs1680488861

NCBI 1000 Genomes Browser:

rs1680488861

Molecular consequence:

NM_001692.4:c.273+2T>A - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Name:: ATP6V1B1-related disorder
Synonyms:: ATP6V1B1-related condition
Identifiers:

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004109865	PreventionGenetics, part of Exact Sciences	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jun 4, 2023)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004109865

PreventionGenetics, part of Exact Sciences

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jun 4, 2023)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

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, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From PreventionGenetics, part of Exact Sciences, SCV004109865.1

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

Description

The ATP6V1B1 c.273+2T>A variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature or in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Variants that disrupt the consensus splice donor site in ATP6V1B1 are expected to be pathogenic. This variant is interpreted 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

Last Updated: Sep 29, 2024

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