NM_001739.2(CA5A):c.473A>C (p.His158Pro) AND Hyperammonemic encephalopathy due to carbonic anhydrase VA deficiency

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Nov 16, 2019
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:: RCV001217769.7

Allele description [Variation Report for NM_001739.2(CA5A):c.473A>C (p.His158Pro)]

NM_001739.2(CA5A):c.473A>C (p.His158Pro)

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.473A>C (p.His158Pro)

HGVS:

NC_000016.10:g.87902507T>G
NG_033227.2:g.39023A>C
NM_001367225.1:c.473A>C
NM_001739.2:c.473A>CMANE SELECT
NP_001354154.1:p.His158Pro
NP_001730.1:p.His158Pro
LRG_1280t1:c.473A>C
LRG_1280:g.39023A>C
LRG_1280p1:p.His158Pro
NC_000016.9:g.87936113T>G
NG_033227.1:g.39000A>C
NM_001739.1:c.473A>C
NR_159798.1:n.552A>C
NR_159799.1:n.433A>C

Protein change:

H158P

Links:

dbSNP: rs754607374

NCBI 1000 Genomes Browser:

rs754607374

Molecular consequence:

NM_001367225.1:c.473A>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001739.2:c.473A>C - missense variant - [Sequence Ontology: SO:0001583]
NR_159798.1:n.552A>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_159799.1:n.433A>C - 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
SCV001389621	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Nov 16, 2019)	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

SCV001389621

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Nov 16, 2019)

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 Labcorp Genetics (formerly Invitae), Labcorp, SCV001389621.4

#	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 (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has not been reported in the literature in individuals 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 ExAC database. This sequence change replaces histidine with proline at codon 158 of the CA5A protein (p.His158Pro). The histidine residue is highly conserved and there is a moderate physicochemical difference between histidine and proline.

#	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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