NM_001739.2(CA5A):c.514G>T (p.Val172Leu) AND Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

This record was updated by the submitter. Please see the current version.

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Aug 9, 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:: RCV001989697.3

Allele description

NM_001739.2(CA5A):c.514G>T (p.Val172Leu)

Gene:

CA5A:carbonic anhydrase 5A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

16q24.2

Genomic location:

Preferred name:

NM_001739.2(CA5A):c.514G>T (p.Val172Leu)

HGVS:

NC_000016.10:g.87902466C>A
NG_033227.2:g.39064G>T
NM_001367225.1:c.514G>T
NM_001739.1:c.514G>T
NM_001739.2:c.514G>TMANE SELECT
NP_001354154.1:p.Val172Leu
NP_001730.1:p.Val172Leu
LRG_1280t1:c.514G>T
LRG_1280:g.39064G>T
LRG_1280p1:p.Val172Leu
NC_000016.9:g.87936072C>A
NR_159798.1:n.593G>T
NR_159799.1:n.474G>T

Protein change:

V172L

Links:

dbSNP: rs142182110

NCBI 1000 Genomes Browser:

rs142182110

Molecular consequence:

NM_001367225.1:c.514G>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001739.2:c.514G>T - missense variant - [Sequence Ontology: SO:0001583]
NR_159798.1:n.593G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159799.1:n.474G>T - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Condition(s)

Name:: Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency
Synonyms:: Carbonic anhydrase VA deficiency, hyperammonemia due to
Identifiers:: MONDO: MONDO:0014332; MedGen: C3810404; Orphanet: 401948; OMIM: 615751

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002284855	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Aug 9, 2022)	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

SCV002284855

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Aug 9, 2022)

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002284855.3

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

Description

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 output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The leucine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. ClinVar contains an entry for this variant (Variation ID: 1495000). This variant has not been reported in the literature in individuals affected with CA5A-related conditions. This variant is present in population databases (rs142182110, gnomAD 0.02%). This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 172 of the CA5A protein (p.Val172Leu).

#	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: May 1, 2024

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