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NM_001739.2(CA5A):c.555G>A (p.Lys185=)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
3 (Most recent: Jan 29, 2019)
Last evaluated:
Sep 28, 2017
Accession:
VCV000127088.2
Variation ID:
127088
Description:
single nucleotide variant
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NM_001739.2(CA5A):c.555G>A (p.Lys185=)

Allele ID
132598
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
16q24.2
Genomic location
16: 87902425 (GRCh38) GRCh38 UCSC
16: 87936031 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000016.10:g.87902425C>T
NC_000016.9:g.87936031C>T
NG_033227.1:g.39082G>A
... more HGVS
Protein change
-
Other names
skippingexon4(p.Leu154_Lys185del)
555G-A
Canonical SPDI
NC_000016.10:87902424:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
The Genome Aggregation Database (gnomAD) 0.00016
Trans-Omics for Precision Medicine (TOPMed) 0.00014
The Genome Aggregation Database (gnomAD), exomes 0.00017
Exome Aggregation Consortium (ExAC) 0.00012
Links
ClinGen: CA345529
OMIM: 114761.0002
dbSNP: rs147623570
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Sep 28, 2017 RCV000483966.2
Pathogenic 2 no assertion criteria provided Jan 8, 2015 RCV000114947.3
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
CA5A - - GRCh38
GRCh37
54 113

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Likely pathogenic
(Sep 28, 2017)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000568852.4
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The c.555G>A variant in the CA5A gene has been reported previously in the homozygous state in association with carbonic anhydrase VA deficiency (van Karnebeek et … (more)
Pathogenic
(Jan 08, 2015)
no assertion criteria provided
Method: literature only
Carbonic anhydrase va deficiency, hyperammonemia due to
Allele origin: germline
GeneReviews
Accession: SCV000221287.1
Submitted: (Jan 08, 2015)
Comment:
mRNA analysis documented an in-frame deletion of exon 4, p.Leu154_Lys185del
Evidence details
Publications
PubMed (1)
Other databases
http://www.ncbi.nlm.nih.gov/book…
Pathogenic
(Mar 06, 2014)
no assertion criteria provided
Method: literature only
CARBONIC ANHYDRASE VA DEFICIENCY, HYPERAMMONEMIA DUE TO
Allele origin: germline
OMIM
Accession: SCV000148851.2
Submitted: (Apr 24, 2014)
Evidence details
Publications
PubMed (1)

Functional evidence

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There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for this variant

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Title Author Journal Year Link
Carbonic Anhydrase VA Deficiency van Karnebeek C - 2021 PMID: 25834911
Mitochondrial carbonic anhydrase VA deficiency resulting from CA5A alterations presents with hyperammonemia in early childhood. van Karnebeek CD American journal of human genetics 2014 PMID: 24530203
http://www.ncbi.nlm.nih.gov/books/NBK284774/ - - - -

Text-mined citations for rs147623570...

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These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 16, 2021