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NM_000071.3(CBS):c.262C>G (p.Pro88Ala) AND Classic homocystinuria

Germline classification:
Uncertain significance (1 submission)
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:
RCV003340518.2

Allele description [Variation Report for NM_000071.3(CBS):c.262C>G (p.Pro88Ala)]

NM_000071.3(CBS):c.262C>G (p.Pro88Ala)

Gene:
CBS:cystathionine beta-synthase [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
NM_000071.3(CBS):c.262C>G (p.Pro88Ala)
HGVS:
  • NC_000021.9:g.43068563G>C
  • NG_008938.1:g.12368C>G
  • NM_000071.3:c.262C>GMANE SELECT
  • NM_001178008.2:c.262C>G
  • NM_001178008.3:c.262C>G
  • NM_001178009.3:c.262C>G
  • NM_001320298.2:c.262C>G
  • NP_000062.1:p.Pro88Ala
  • NP_000062.1:p.Pro88Ala
  • NP_001171479.1:p.Pro88Ala
  • NP_001171480.1:p.Pro88Ala
  • NP_001307227.1:p.Pro88Ala
  • LRG_777t1:c.262C>G
  • LRG_777:g.12368C>G
  • LRG_777p1:p.Pro88Ala
  • NC_000021.8:g.44488673G>C
  • NM_000071.2:c.262C>G
Protein change:
P88A
Molecular consequence:
  • NM_000071.3:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178008.3:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178009.3:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320298.2:c.262C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Classic homocystinuria
Synonyms:
HOMOCYSTINURIA WITH OR WITHOUT RESPONSE TO PYRIDOXINE; Homocystinuria due to CBS deficiency; Homocystinuria due to cystathionine beta-synthase deficiency; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0009352; MedGen: C0751202; Orphanet: 394; OMIM: 236200

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004047692Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV004047692.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The missense variant c.262C>G (p.Pro88Ala) in CBS gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Pro88Ala variant is novel (not in any individuals) in gnomAD Exomes and 1000 Genomes. The amino acid Pro at position 88 is changed to a Ala changing protein sequence and it might alter its composition and physico-chemical properties. The variant is predicted to be damaging by both SIFT and PolyPhen2. The residue is conserved across species. The amino acid change p.Pro88Ala in CBS is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

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

Last Updated: Sep 29, 2024