NM_001739.2(CA5A):c.555G>A (p.Lys185=) AND not provided

Clinical significance:Likely pathogenic (Last evaluated: Sep 28, 2017)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:
current
Accession:
RCV000483966.2

Allele description [Variation Report for NM_001739.2(CA5A):c.555G>A (p.Lys185=)]

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

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.555G>A (p.Lys185=)
Other names:
skippingexon4(p.Leu154_Lys185del)
HGVS:
  • NC_000016.10:g.87902425C>T
  • NG_033227.1:g.39082G>A
  • NG_033227.2:g.39105G>A
  • NM_001367225.1:c.555G>A
  • NM_001739.2:c.555G>AMANE SELECT
  • NP_001354154.1:p.Lys185=
  • NP_001730.1:p.Lys185=
  • LRG_1280t1:c.555G>A
  • LRG_1280:g.39105G>A
  • LRG_1280p1:p.Lys185=
  • NC_000016.9:g.87936031C>T
  • NM_001739.1:c.555G>A
  • NR_159798.1:n.634G>A
  • NR_159799.1:n.515G>A
Nucleotide change:
555G-A
Links:
OMIM: 114761.0002; dbSNP: rs147623570
NCBI 1000 Genomes Browser:
rs147623570
Molecular consequence:
  • NR_159798.1:n.634G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_159799.1:n.515G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_001367225.1:c.555G>A - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001739.2:c.555G>A - synonymous variant - [Sequence Ontology: SO:0001819]

Condition(s)

Identifiers:
MedGen: CN517202

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000568852GeneDxcriteria provided, single submitter
Likely pathogenic
(Sep 28, 2017)
germlineclinical testing

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000568852.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

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 al., 2014). The c.555G>A variant is predicted to destroy the natural splice donor site in intron 4 and studies indicate it results in deletion of exon 4 that includes residues in the active site of the CA5A enzyme (van Karnebeek et al., 2014). In addition, functional studies of the c.555G>A variant demonstrated absent enzyme activity and altered thermal stability (van Karnebeek et al., 2014; Diez-Fernandez et al., 2016). The c.555G>A variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The c.555G>A variant is a strong candidate for a pathogenic variant, however the possibility it may be a rare benign variant cannot be excluded.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Oct 16, 2021

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