NM_001692.4(ATP6V1B1):c.175-1G>C AND not provided

Germline classification:: Pathogenic (4 submissions)
Last evaluated:: Feb 22, 2021
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:: RCV001702561.10

Allele description [Variation Report for NM_001692.4(ATP6V1B1):c.175-1G>C]

NM_001692.4(ATP6V1B1):c.175-1G>C

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.175-1G>C

HGVS:

NC_000002.12:g.70958045G>C
NG_008016.1:g.27178G>C
NM_001692.4:c.175-1G>CMANE SELECT
LRG_1176t1:c.175-1G>C
LRG_1176:g.27178G>C
NC_000002.11:g.71185175G>C
NM_001692.3:c.175-1G>C

Links:

dbSNP: rs1572919267

NCBI 1000 Genomes Browser:

rs1572919267

Molecular consequence:

NM_001692.4:c.175-1G>C - splice acceptor variant - [Sequence Ontology: SO:0001574]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001931219	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001952872	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV001980179	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Pathogenic	germline	clinical testing
SCV002245892	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Feb 22, 2021)	germline	clinical testing	PubMed (7) [See all records that cite these PMIDs] 16611712, 25285676, 31733597, 16199547, 9916796, 18368028, 28492532

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

Genetic investigation of autosomal recessive distal renal tubular acidosis: evidence for early sensorineural hearing loss associated with mutations in the ATP6V0A4 gene.

Vargas-Poussou R, Houillier P, Le Pottier N, Strompf L, Loirat C, Baudouin V, Macher MA, Déchaux M, Ulinski T, Nobili F, Eckart P, Novo R, Cailliez M, Salomon R, Nivet H, Cochat P, Tack I, Fargeot A, Bouissou F, Kesler GR, Lorotte S, Godefroid N, et al.

J Am Soc Nephrol. 2006 May;17(5):1437-43. Epub 2006 Apr 12.

PubMed [citation]

PMID:: 16611712

Molecular investigation of distal renal tubular acidosis in Tunisia, evidence for founder mutations.

Nagara M, Voskarides K, Nouira S, Ben Halim N, Kefi R, Aloulou H, Romdhane L, Ben Abdallah R, Ben Rhouma F, Aissa K, Boughamoura L, Kammoun T, Azzouz H, Abroug S, Ben Turkia H, Ayadi A, Mrad R, Chabchoub I, Hachicha M, Chemli J, Deltas C, Abdelhak S.

Genet Test Mol Biomarkers. 2014 Nov;18(11):741-8. doi: 10.1089/gtmb.2014.0175. Epub 2014 Oct 6.

PubMed [citation]

PMID:: 25285676
PMCID:: PMC4217022

See all PubMed Citations (7)

Details of each submission

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001931219.1

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

#	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

From Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ - VKGL Data-share Consensus, SCV001952872.1

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

#	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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001980179.1

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

#	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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002245892.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (7)

Description

For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. This variant has been observed in individual(s) with distal renal tubular acidosis (dRTA) with sensorineural hearing loss (PMID: 16611712, 25285676, 31733597). It has also been observed to segregate with disease in related individuals. This variant is also known as IVS2-1G>C. ClinVar contains an entry for this variant (Variation ID: 638151). This variant is not present in population databases (ExAC no frequency). This sequence change affects an acceptor splice site in intron 2 of the ATP6V1B1 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 ATP6V1B1 are known to be pathogenic (PMID: 9916796, 18368028).

#	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

ClinVar

Relating variation to medicine