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NM_000071.3(CBS):c.1330G>A (p.Asp444Asn) AND HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Jan 29, 2024
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:
RCV000000149.17

Allele description [Variation Report for NM_000071.3(CBS):c.1330G>A (p.Asp444Asn)]

NM_000071.3(CBS):c.1330G>A (p.Asp444Asn)

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.1330G>A (p.Asp444Asn)
Other names:
p.D444N:GAC>AAC; NM_000071.2(CBS):c.1330G>A(p.Asp444Asn); NM_001178008.1(CBS):c.1330G>A(p.Asp444Asn); NM_001178009.1(CBS):c.1330G>A(p.Asp444Asn)
HGVS:
  • NC_000021.9:g.43058862C>T
  • NG_008938.1:g.22069G>A
  • NM_000071.3:c.1330G>AMANE SELECT
  • NM_001178008.3:c.1330G>A
  • NM_001178009.3:c.1330G>A
  • NM_001320298.2:c.1330G>A
  • NM_001321072.1:c.1015G>A
  • NP_000062.1:p.Asp444Asn
  • NP_000062.1:p.Asp444Asn
  • NP_001171479.1:p.Asp444Asn
  • NP_001171480.1:p.Asp444Asn
  • NP_001307227.1:p.Asp444Asn
  • NP_001308001.1:p.Asp339Asn
  • LRG_777t1:c.1330G>A
  • LRG_777:g.22069G>A
  • LRG_777p1:p.Asp444Asn
  • NC_000021.8:g.44478972C>T
  • NM_000071.2:c.1330G>A
  • P35520:p.Asp444Asn
Protein change:
D339N; ASP444ASN
Links:
UniProtKB: P35520#VAR_002192; OMIM: 613381.0010; dbSNP: rs28934891
NCBI 1000 Genomes Browser:
rs28934891
Molecular consequence:
  • NM_000071.3:c.1330G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178008.3:c.1330G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001178009.3:c.1330G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001320298.2:c.1330G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001321072.1:c.1015G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED
Identifiers:
MedGen: C3150344

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000020292OMIM
no assertion criteria provided
Pathogenic
(Jan 1, 2004)
germlineliterature only

PubMed (3)
[See all records that cite these PMIDs]

SCV000543508Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 29, 2024)
germlineclinical testing

PubMed (10)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Stroke in young patients with hyperhomocysteinemia due to cystathionine beta-synthase deficiency.

Kelly PJ, Furie KL, Kistler JP, Barron M, Picard EH, Mandell R, Shih VE.

Neurology. 2003 Jan 28;60(2):275-9.

PubMed [citation]
PMID:
12552044
See all PubMed Citations (11)

Details of each submission

From OMIM, SCV000020292.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (3)

Description

Homocystinuria

In a 20-year-old woman with pyridoxine-responsive homocystinuria (236200), Kluijtmans et al. (1996) identified a homozygous 1330G-A transition in the CBS gene, resulting in an asp444-to-asn (D444N) substitution in the regulatory domain of the protein. She was first admitted to the hospital at the age of 9 years because of psychomotor retardation, marfanoid features with excessive height, dolichostenomelia, arachnodactyly, and homocystinuria. She was treated with pyridoxine, folic acid, and betaine, with favorable results. Eleven years later she was in very good physical condition and her intellectual development had reached an average level. Ectopia lentis, osteoporosis, and vascular complications had not occurred. Both parents and an unaffected sister were heterozygous for the mutation. Despite the homozygous mutation, CBS activities in extracts of cultured fibroblasts of this patient were not in the homozygous but in the heterozygous range. In vitro functional expression studies showed no stimulation of CBS activity by S-adenosylmethionine, contrary to a 3-fold stimulation in control fibroblast extract. These data suggested that the D444N mutation interfered with S-adenosylmethionine regulation of CBS. Furthermore, it indicated the importance of S-adenosylmethionine regulation of the transsulfuration pathway in homocysteine homeostasis in humans.

CBS domains are defined as sequence motifs that occur in several different proteins in all kingdoms of life. Their functional importance is underlined by the finding that mutations in conserved residues within them cause a variety of human hereditary diseases, including homocystinuria. Scott et al. (2004) showed that tandem pairs of CBS domains from cystathionine beta-synthase, as well as the CBS domains from at least 3 other proteins that are the sites of mutations causing hereditary diseases, bind AMP, ATP, or S-adenosylmethionine, whereas mutations that cause hereditary diseases impair this binding. An interesting feature of the pathogenic mutations in CBS domains is that they tend to occur in equivalent positions. Thus, 3 mutations in the PRKAG2 gene that cause disease--R302Q (602743.0001), H383R, and R531G (602743.0006)--all align (plus or minus 1 residue) with the D444N mutation in the CBS gene.

Hyperhomocysteinemia, Thrombotic, CBS-related

In a patient with early-onset stroke and hyperhomocysteinemia without other manifestations of homocystinuria (see 236200), Kelly et al. (2003) identified a heterozygous D444N mutation. The patient was a 39-year-old Venezuelan man who had a retinal artery occlusion due to an arterial dissection. An unaffected sister was also heterozygous for the mutation. The presence of a second mutation could not be excluded.

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

From Labcorp Genetics (formerly Invitae), Labcorp, SCV000543508.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (10)

Description

This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 444 of the CBS protein (p.Asp444Asn). This variant is present in population databases (rs28934891, gnomAD 0.1%). This missense change has been observed in individual(s) with homocystinuria (PMID: 8755636, 14972327, 16479318, 21520339). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 126). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CBS protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects CBS function (PMID: 8755636, 14722619, 20490928, 20506325, 22069143, 25044645). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Oct 26, 2024