NM_000071.3(CBS):c.19dup (p.Gln7fs) AND Classic homocystinuria

Germline classification:: Pathogenic (5 submissions)
Last evaluated:: Mar 15, 2024
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:: RCV000409151.10

Allele description [Variation Report for NM_000071.3(CBS):c.19dup (p.Gln7fs)]

NM_000071.3(CBS):c.19dup (p.Gln7fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

21q22.3

Genomic location:

Preferred name:

NM_000071.3(CBS):c.19dup (p.Gln7fs)

HGVS:

NC_000021.8:g.44492284_44492285insG
NC_000021.9:g.43072180dup
NG_008938.1:g.8756dup
NM_000071.3:c.19dupMANE SELECT
NM_001178008.3:c.19dup
NM_001178009.3:c.19dup
NM_001320298.2:c.19dup
NP_000062.1:p.Gln7fs
NP_000062.1:p.Gln7fs
NP_001171479.1:p.Gln7fs
NP_001171480.1:p.Gln7fs
NP_001307227.1:p.Gln7fs
LRG_777t1:c.19dup
LRG_777:g.8756dup
LRG_777p1:p.Gln7fs
NC_000021.8:g.44492284_44492285insG
NC_000021.8:g.44492290dup
NC_000021.8:g.44492290dupG
NM_000071.2:c.19dup
NM_000071.2:c.19dupC
NM_000071.3:c.19dupCMANE SELECT

Protein change:

Q7fs

Links:

dbSNP: rs748695461

NCBI 1000 Genomes Browser:

rs748695461

Molecular consequence:

NM_000071.3:c.19dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001178008.3:c.19dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001178009.3:c.19dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001320298.2:c.19dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV000486905	Counsyl	criteria provided, single submitter (Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015))	Pathogenic (Sep 2, 2016)	unknown	clinical testing	PubMed (3) [See all records that cite these PMIDs] 25218699, 12124992, 11359213 mdi-5618_320494_Counsyl Autosomal and X-linked Recessive Disease Classification criteria (2015).pdf, Citation Link,
SCV001163821	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 15, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002083836	Natera, Inc.	no assertion criteria provided	Pathogenic (Oct 14, 2020)	germline	clinical testing
SCV002809450	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 5, 2021)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004175216	Genetics and Molecular Pathology, SA Pathology See additional submitters Shariant Australia, Australian Genomics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 5, 2021)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

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Summary from all submissions

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

Enzymatic diagnosis of homocystinuria by determination of cystathionine-ß-synthase activity in plasma using LC-MS/MS.

Alcaide P, Krijt J, Ruiz-Sala P, Ješina P, Ugarte M, Kožich V, Merinero B.

Clin Chim Acta. 2015 Jan 1;438:261-5. doi: 10.1016/j.cca.2014.09.009. Epub 2014 Sep 16.

PubMed [citation]

PMID:: 25218699

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 (4)

Details of each submission

From Counsyl, SCV000486905.2

#	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 Baylor Genetics, SCV001163821.2

#	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

From Natera, Inc., SCV002083836.1

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

#	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 Fulgent Genetics, Fulgent Genetics, SCV002809450.1

#	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

From Genetics and Molecular Pathology, SA Pathology, SCV004175216.1

#	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	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Oct 13, 2024

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