NM_000071.3(CBS):c.258dup (p.Thr87fs) AND HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 2, 2023
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:: RCV003495869.2

Allele description [Variation Report for NM_000071.3(CBS):c.258dup (p.Thr87fs)]

NM_000071.3(CBS):c.258dup (p.Thr87fs)

Gene:

CBS:cystathionine beta-synthase [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_000071.3(CBS):c.258dup (p.Thr87fs)

HGVS:

NC_000021.9:g.43068567dup
NG_008938.1:g.12364dup
NM_000071.3:c.258dupMANE SELECT
NM_001178008.3:c.258dup
NM_001178009.3:c.258dup
NM_001320298.2:c.258dup
NP_000062.1:p.Thr87Hisfs
NP_000062.1:p.Thr87fs
NP_001171479.1:p.Thr87fs
NP_001171480.1:p.Thr87fs
NP_001307227.1:p.Thr87fs
LRG_777t1:c.258dup
LRG_777:g.12364dup
LRG_777p1:p.Thr87Hisfs
NC_000021.8:g.44488676_44488677insG
NC_000021.8:g.44488677dup
NM_000071.2:c.258dup

Protein change:

T87fs

Molecular consequence:

NM_000071.3:c.258dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001178008.3:c.258dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001178009.3:c.258dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001320298.2:c.258dup - frameshift variant - [Sequence Ontology: SO:0001589]

Condition(s)

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

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esv3595011 (1)
dbVar
cytochrome oxidase subunit 1, partial (mitochondrion) [Cyphorhinus arada]
cytochrome oxidase subunit 1, partial (mitochondrion) [Cyphorhinus arada]
gi|402712656|gb|AFQ92224.1|

Protein
Homo sapiens leucine rich repeat containing 19 (LRRC19), mRNA
Homo sapiens leucine rich repeat containing 19 (LRRC19), mRNA
gi|1653961233|ref|NM_022901.3|

Nucleotide
hypothetical protein DDB_G0288501 [Dictyostelium discoideum AX4]
hypothetical protein DDB_G0288501 [Dictyostelium discoideum AX4]
gi|66805957|ref|XP_636700.1||gnl|RE :AAFI|DDB0233432

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004320688	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 2, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 10338090, 12124992, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004320688

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 2, 2023)

germline

clinical testing

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

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

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

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

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004320688.1

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with CBS-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Thr87Hisfs*18) in the CBS gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CBS are known to be pathogenic (PMID: 10338090, 12124992).

#	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

Last Updated: Sep 29, 2024

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