Variant chr21-43065499-CCCAGTGCCCGCAGCACGT-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Pathogenic. Variant got 13 ACMG points: 13P and 0B. PM2PM4PP3PP5_Very_Strong

The NM_000071.3(CBS):c.536_553delACGTGCTGCGGGCACTGG(p.Asp179_Leu184del) variant causes a disruptive inframe deletion change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000487 in 410,816 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely pathogenic (★★).

Frequency

Genomes: not found (cov: 4)

Exomes 𝑓: 0.0000049 ( 0 hom. )

Consequence

CBS
NM_000071.3 disruptive_inframe_deletion

Scores

Not classified

Clinical Significance

Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:6U:1

Conservation

PhyloP100: 7.79

Variant links:

Genes affected

CBS (HGNC:1550): (cystathionine beta-synthase) The protein encoded by this gene acts as a homotetramer to catalyze the conversion of homocysteine to cystathionine, the first step in the transsulfuration pathway. The encoded protein is allosterically activated by adenosyl-methionine and uses pyridoxal phosphate as a cofactor. Defects in this gene can cause cystathionine beta-synthase deficiency (CBSD), which can lead to homocystinuria. This gene is a major contributor to cellular hydrogen sulfide production. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2016]

CBS links:

CBS (HGNC:):

CBS links:

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ACMG classification

Classification made for transcript

Verdict is Pathogenic. Variant got 13 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

PM4

Nonframeshift variant in NON repetitive region in NM_000071.3.

PP3

No computational evidence supports a deleterious effect, but strongly conserved according to phyloP

PP5

Variant 21-43065499-CCCAGTGCCCGCAGCACGT-C is Pathogenic according to our data. Variant chr21-43065499-CCCAGTGCCCGCAGCACGT-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 198388.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-43065499-CCCAGTGCCCGCAGCACGT-C is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CBS	NM_000071.3 linkuse as main transcript	c.536_553delACGTGCTGCGGGCACTGG	p.Asp179_Leu184del	disruptive_inframe_deletion	7/17	ENST00000398165.8	NP_000062.1	P35520-1Q9NTF0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CBS	ENST00000398165.8 linkuse as main transcript	c.536_553delACGTGCTGCGGGCACTGG	p.Asp179_Leu184del	disruptive_inframe_deletion	7/17	1	NM_000071.3	ENSP00000381231.4		P35520-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000121

AC:

AN:

248946

Hom.:

AF XY:

0.0000148

AC XY:

AN XY:

134784

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000268

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000487

AC:

AN:

410816

Hom.:

AF XY:

0.00

AC XY:

AN XY:

217014

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000878

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:6Uncertain:1

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Classic homocystinuria

Pathogenic:3

Likely pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Apr 02, 2021	- -
Likely pathogenic, no assertion criteria provided	clinical testing	Counsyl	Dec 19, 2018	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Nov 17, 2023	- -

not provided

Pathogenic:1Uncertain:1

Uncertain significance, flagged submission	clinical testing	Eurofins Ntd Llc (ga)	Aug 28, 2014	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Sep 22, 2016	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. -

Familial thoracic aortic aneurysm and aortic dissection

Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 03, 2022

The c.536_553del18 (p.D179_L184del) alteration is located in exon 7 (coding exon 5) of the CBS gene. This alteration consists of an in-frame deletion of 18 nucleotides between nucleotide positions c.536 and c.553, resulting in the deletion of <NA> residues. This variant was not reported in population-based cohorts in the Genome Aggregation Database (gnomAD). This variant has been reported in several individuals with CBS-related homocystinuria and a second variant (Ruhoy, 2014; Gaustadnes, 2002) including one individual with a dislocated lens, mild developmental delay and intellectual disability and a Marfanoid habitus (Gaustadnes, 2002). This alteration is predicted to be deleterious by in silico analysis (Choi, 2012). Based on the available evidence, this alteration is classified as likely pathogenic. -

HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED

Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 20, 2023

This variant, c.536_553del, results in the deletion of 6 amino acid(s) of the CBS protein (p.Asp179_Leu184del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs794727835, gnomAD 0.003%). This variant has been observed in individual(s) with CBS-deficiency (PMID: 12124992, 24138954; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 198388). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. For these reasons, this variant has been classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

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