NM_001739.2(CA5A):c.149C>A (p.Pro50Gln) AND Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: May 27, 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:: RCV002667907.4

Allele description [Variation Report for NM_001739.2(CA5A):c.149C>A (p.Pro50Gln)]

NM_001739.2(CA5A):c.149C>A (p.Pro50Gln)

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.149C>A (p.Pro50Gln)

HGVS:

NC_000016.10:g.87926939G>T
NG_033227.2:g.14591C>A
NM_001367225.1:c.149C>A
NM_001739.2:c.149C>AMANE SELECT
NP_001354154.1:p.Pro50Gln
NP_001730.1:p.Pro50Gln
LRG_1280t1:c.149C>A
LRG_1280:g.14591C>A
LRG_1280p1:p.Pro50Gln
NC_000016.9:g.87960545G>T
NR_159798.1:n.228C>A
NR_159799.1:n.228C>A

Protein change:

P50Q

Molecular consequence:

NM_001367225.1:c.149C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001739.2:c.149C>A - missense variant - [Sequence Ontology: SO:0001583]
NR_159798.1:n.228C>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159799.1:n.228C>A - 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
SCV002987142	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (May 27, 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

SCV002987142

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(May 27, 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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV002987142.2

#	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 are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals affected with CA5A-related conditions. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces proline, which is neutral and non-polar, with glutamine, which is neutral and polar, at codon 50 of the CA5A protein (p.Pro50Gln).

#	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 28, 2024

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