U.S. flag

An official website of the United States government

NM_000071.3(CBS):c.536_553del (p.Asp179_Leu184del) AND not provided

Germline classification:
Likely pathogenic (2 submissions)
Last evaluated:
Sep 22, 2016
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:
RCV000413538.8

Allele description [Variation Report for NM_000071.3(CBS):c.536_553del (p.Asp179_Leu184del)]

NM_000071.3(CBS):c.536_553del (p.Asp179_Leu184del)

Gene:
CBS:cystathionine beta-synthase [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
21q22.3
Genomic location:
Preferred name:
NM_000071.3(CBS):c.536_553del (p.Asp179_Leu184del)
HGVS:
  • NC_000021.9:g.43065503_43065520del
  • NG_008938.1:g.15414_15431del
  • NM_000071.3:c.536_553delMANE SELECT
  • NM_001178008.3:c.536_553del
  • NM_001178009.3:c.536_553del
  • NM_001320298.2:c.536_553del
  • NM_001321072.1:c.221_238del
  • NP_000062.1:p.Asp179_Leu184del
  • NP_000062.1:p.Asp179_Leu184del
  • NP_001171479.1:p.Asp179_Leu184del
  • NP_001171480.1:p.Asp179_Leu184del
  • NP_001307227.1:p.Asp179_Leu184del
  • NP_001308001.1:p.Asp74_Leu79del
  • LRG_777t1:c.536_553del
  • LRG_777:g.15414_15431del
  • LRG_777p1:p.Asp179_Leu184del
  • NC_000021.8:g.44485610_44485627del
  • NC_000021.8:g.44485613_44485630del
  • NM_000071.2:c.536_553del
  • NM_000071.2:c.536_553del18
  • NM_000071.2:c.536_553delACGTGCTGCGGGCACTGG
  • p.(D179_L184del)
Links:
dbSNP: rs794727835
NCBI 1000 Genomes Browser:
rs794727835
Molecular consequence:
  • NM_000071.3:c.536_553del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001178008.3:c.536_553del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001178009.3:c.536_553del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001320298.2:c.536_553del - inframe_deletion - [Sequence Ontology: SO:0001822]
  • NM_001321072.1:c.221_238del - inframe_deletion - [Sequence Ontology: SO:0001822]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000491080GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Likely pathogenic
(Sep 22, 2016) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknown1not providednot providednot providednot providedclinical testing

Citations

PubMed

Cystathionine beta-synthase mutations in homocystinuria.

Kraus JP, Janosík M, Kozich V, Mandell R, Shih V, Sperandeo MP, Sebastio G, de Franchis R, Andria G, Kluijtmans LA, Blom H, Boers GH, Gordon RB, Kamoun P, Tsai MY, Kruger WD, Koch HG, Ohura T, Gaustadnes M.

Hum Mutat. 1999;13(5):362-75. Review.

PubMed [citation]
PMID:
10338090

Details of each submission

From Eurofins Ntd Llc (ga), SCV000232001.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot provided1not providednot providednot provided

From GeneDx, SCV000491080.1

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

Description

The c.536_553del18 variant in the CBS gene has been reported in patients with homocystinuria due to CBS deficiency (Kraus et al. 1999; Ruhoy et al. 2014). This variant results in an in-frame deletion of 6 amino acids starting at codon Aspartic acid 179, denoted p.D179_L184. This deletion occurs in a conserved region of the CBS protein and other in-frame deletions in CBS have been reported in the Human Gene Mutation Database (HGMD) in association with homocystinuria due to CBS deficiency (Stenson et al., 2014). The c.536_553del18 variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. In summary, we interpret c.536_553del18 to be likely pathogenic.

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

Flagged submissions

Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000232001Eurofins Ntd Llc (ga)
flagged submission
Reason: Outlier claim with insufficient supporting evidence
Notes: None

(EGL Classification Definitions 2015)		Uncertain significance
(Aug 28, 2014) 		germlineclinical testing

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

Citation Link

Last Updated: Nov 3, 2024