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

Germline classification:: Likely pathogenic (3 submissions)
Last evaluated:: Nov 17, 2023
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000675172.13

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]

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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000800795	Counsyl	no assertion criteria provided	Likely pathogenic (Dec 19, 2018)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 12124992, 10338090, 24138954
SCV002025087	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 2, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004215552	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Nov 17, 2023)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV000800795

Counsyl

no assertion criteria provided

Likely pathogenic
(Dec 19, 2018)

unknown

clinical testing

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

SCV002025087

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 2, 2021)

germline

clinical testing

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

SCV004215552

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Nov 17, 2023)

unknown

clinical testing

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

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

The molecular basis of cystathionine beta-synthase deficiency in Australian patients: genotype-phenotype correlations and response to treatment.

Gaustadnes M, Wilcken B, Oliveriusova J, McGill J, Fletcher J, Kraus JP, Wilcken DE.

Hum Mutat. 2002 Aug;20(2):117-26.

PubMed [citation]

PMID:: 12124992

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

See all PubMed Citations (4)

Details of each submission

From Counsyl, SCV000800795.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV002025087.3

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004215552.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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