NM_020632.3(ATP6V0A4):c.1571C>T (p.Pro524Leu) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 5, 2022
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:: RCV002512809.2

Allele description [Variation Report for NM_020632.3(ATP6V0A4):c.1571C>T (p.Pro524Leu)]

NM_020632.3(ATP6V0A4):c.1571C>T (p.Pro524Leu)

Gene:

ATP6V0A4:ATPase H+ transporting V0 subunit a4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q34

Genomic location:

Preferred name:

NM_020632.3(ATP6V0A4):c.1571C>T (p.Pro524Leu)

HGVS:

NC_000007.14:g.138739541G>A
NG_008145.1:g.63656C>T
NM_020632.3:c.1571C>TMANE SELECT
NM_130840.3:c.1571C>T
NM_130841.3:c.1571C>T
NP_065683.2:p.Pro524Leu
NP_570855.2:p.Pro524Leu
NP_570856.2:p.Pro524Leu
LRG_1175t1:c.1571C>T
LRG_1175:g.63656C>T
LRG_1175p1:p.Pro524Leu
NC_000007.13:g.138424286G>A
NM_020632.2:c.1571C>T
Q9HBG4:p.Pro524Leu

Protein change:

P524L; PRO524LEU

Links:

UniProtKB: Q9HBG4#VAR_017255; OMIM: 605239.0008; dbSNP: rs121908368

NCBI 1000 Genomes Browser:

rs121908368

Molecular consequence:

NM_020632.3:c.1571C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_130840.3:c.1571C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_130841.3:c.1571C>T - missense variant - [Sequence Ontology: SO:0001583]

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
SCV003440222	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jul 5, 2022)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10973252, 19364879, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003440222

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jul 5, 2022)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

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

Mutations in ATP6N1B, encoding a new kidney vacuolar proton pump 116-kD subunit, cause recessive distal renal tubular acidosis with preserved hearing.

Smith AN, Skaug J, Choate KA, Nayir A, Bakkaloglu A, Ozen S, Hulton SA, Sanjad SA, Al-Sabban EA, Lifton RP, Scherer SW, Karet FE.

Nat Genet. 2000 Sep;26(1):71-5.

PubMed [citation]

PMID:: 10973252

Medullary sponge kidney associated with primary distal renal tubular acidosis and mutations of the H+-ATPase genes.

Carboni I, Andreucci E, Caruso MR, Ciccone R, Zuffardi O, Genuardi M, Pela I, Giglio S.

Nephrol Dial Transplant. 2009 Sep;24(9):2734-8. doi: 10.1093/ndt/gfp160. Epub 2009 Apr 13.

PubMed [citation]

PMID:: 19364879

See all PubMed Citations (3)

Details of each submission

From Invitae, SCV003440222.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This missense change has been observed in individual(s) with distal renal tubular acidosis (PMID: 10973252, 19364879). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs121908368, gnomAD 0.01%). This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 524 of the ATP6V0A4 protein (p.Pro524Leu). ClinVar contains an entry for this variant (Variation ID: 5157). 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. Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0").

#	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: Feb 14, 2024

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