21-43065645-C-T

Variant names:

• chr21-43065645-C-T
• rs121964970
• NM_000071.3:c.502G>A

Variant summary

Our verdict is Likely pathogenic. Variant got 8 ACMG points: 9P and 1B. PM1 PM5 PP3_Strong PP5 BS2_Supporting

The NM_000071.3(CBS):​c.502G>A​(p.Val168Met) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. V168A) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 0)
  • Exomes 𝑓: 0.000040 (3 hom.)
• Consequence: CBS NM_000071.3 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:6 U:4
• Conservation: PhyloP100: 6.78

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]

ACMG classification

Verdict is Likely_pathogenic. Variant got 8 ACMG points.

• PM1: In a strand (size 6) in uniprot entity CBS_HUMAN there are 4 pathogenic changes around while only 0 benign (100%) in NM_000071.3
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.984
• PP5: Variant 21-43065645-C-T is Pathogenic according to our data. Variant chr21-43065645-C-T is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 127.We mark this variant Likely_pathogenic, oryginal submissions are: {Likely_pathogenic=4, Uncertain_significance=3, Pathogenic=1}. Variant chr21-43065645-C-T is described in Lovd as [Pathogenic].
• BS2: High Homozygotes in GnomAdExome4 at 3 AR geneVariant has number of homozygotes lower than other variant known as pathogenic in the gene, so the strength is limited to Supporting.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBS	NM_000071.3	c.502G>A	p.Val168Met	missense_variant	Exon 6 of 17	ENST00000398165.8	NP_000062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBS	ENST00000398165.8	c.502G>A	p.Val168Met	missense_variant	Exon 6 of 17	1	NM_000071.3	ENSP00000381231.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.0000107 AC: 2 AN: 186900 Hom.: 0 AF XY: 0.0000200 AC XY: 2 AN XY: 100190

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: 0.0000400

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000128

Gnomad OTH exome AF: 0.00

GnomAD4 exome AF: 0.0000402 AC: 12 AN: 298308 Hom.: 3 Cov.: 0 AF XY: 0.0000509 AC XY: 8 AN XY: 157194

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: 0.000198

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.0000122

Gnomad4 OTH exome AF: 0.000118

GnomAD4 genome Cov.: 0

ExAC AF: 0.00000835 AC: 1

Asia WGS AF: 0.000289 AC: 1 AN: 3478

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Pathogenic:6 Uncertain:4

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Classic homocystinuria Pathogenic:2 Uncertain:2

-

Neuberg Centre For Genomic Medicine, NCGM

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The missense c.502G>A (p.Val168Met) variant in CBS gene has been reported in individuals with Homocystinuria cystathionine beta synthase (CBS) deficiency (Hua N et al. 2021; Kaadan MI et al. 2018). Experimental studies have shown that this missense change affects CBS function (Mayfield JA et al. 2012). The p.Val168Met variant has allele frequency 0.001% in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has been reported to the ClinVar database as Uncertain significance / Pathogenic / Likely Pathogenic (multiple submiters). The amino acid change p.Val168Met in CBS is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Val at position 168 is changed to a Met changing protein sequence and it might alter its composition and physico-chemical properties. Functional studies are required to prove the pathogenicity for the variant. For these reasons, this variant has been classified as Likely Pathogenic. -

Mar 05, 2020

Natera, Inc.

Significance: Uncertain significance

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Apr 27, 2017

Illumina Laboratory Services, Illumina

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Feb 08, 2024

Baylor Genetics

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

not provided Pathogenic:1 Uncertain:1

Aug 29, 2017

Eurofins Ntd Llc (ga)

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

May 19, 2021

GeneDx

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Has been reported in individuals with B6-responsive homocystinuria (Kruger et al., 1995; Shan et al., 1998), as well as an individual with spontaneous coronary artery dissection (SCAD) (Kaadan et al., 2018).; Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies in yeast have demonstrated that V168M results in a non-functional allele with impaired CBS function (Shan et al., 1998; Mayfield et al., 2012).; Reported in ClinVar (ClinVar Variant ID# 127; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 10338090, 10531322, 31301157, 8528202, 22267502, 29650765, 9590298, 11230183, 20066033) -

Homocystinuria, pyridoxine-responsive Pathogenic:1

Dec 01, 2003

OMIM

Significance: Pathogenic

Review Status: no assertion criteria provided

Collection Method: literature only

- -

HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED Pathogenic:1

Aug 01, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

This sequence change replaces valine, which is neutral and non-polar, with methionine, which is neutral and non-polar, at codon 168 of the CBS protein (p.Val168Met). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This missense change has been observed in individual(s) with clinical features of CBS-related conditions and/or homocystinuria due to cystathionine beta-synthase deficiency (PMID: 8528202, 33985475; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 127). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CBS protein function with a positive predictive value of 95%. Experimental studies have shown that this missense change affects CBS function (PMID: 8528202, 10531322, 20066033, 22267502). For these reasons, this variant has been classified as Pathogenic. -

Homocystinuria Pathogenic:1

Mar 09, 2024

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Significance: Likely pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

Variant summary: CBS c.502G>A (p.Val168Met) results in a conservative amino acid change located in the Pyridoxal-phosphate dependent enzyme domain (IPR001926) of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 1.1e-05 in 186900 control chromosomes. c.502G>A has been reported in the literature as a non-informative genotype in CBS cell lines, in presumed compound heterozygosity in an individual with Spontaneous Coronary Artery Dissection and as a confirmed compound heterozygous genotype in an individual presenting with Recurrent dislocation of binocular crystal lenses and cystathionine beta synthase deficiency (example, Kruger_1995, Kaadan_2018, Hua_2021). At least two publications report experimental evidence evaluating an impact on protein function (example, Kabil_1999, Singh_2010). The most pronounced variant effect results in <10% of normal cystathionine beta synthase activity in vitro. The following publications have been ascertained in the context of this evaluation (PMID: 33985475, 29650765, 10531322, 8528202, 22267502, 20066033). ClinVar contains an entry for this variant (Variation ID: 127). Based on the evidence outlined above, the variant was classified as likely pathogenic. -

Familial thoracic aortic aneurysm and aortic dissection Uncertain:1

Aug 22, 2019

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The p.V168M pathogenic mutation (also known as c.502G>A), located in coding exon 4 of the CBS gene, results from a G to A substitution at nucleotide position 502. The valine at codon 168 is replaced by methionine, an amino acid with highly similar properties. This variant was first reported as detected in cell lines from an individual with inferred clinical phenotype of homozygous CBS enzyme deficiency; however, clinical details were not provided, this variant was detected in the heterozygous state, and the potential of sample and clinical information misclassification was suggested (Kruger WD et al. Hum Mol Genet. 1995;4:1155-61). This variant was also detected in an individual from a coronary artery dissection cohort who had a second CBS variant (phase unknown), no typical disease features, and normal serum homocysteine levels (Kaadan MI et al. Circ Genom Precis Med. 2018;11:e001933). Studies have indicated that this variant results in reduced protein and enzyme activity in yeast assays (Kabil O et al. J Biol Chem. 1999;274:31256-60; Shan X et al. Hum Mol Genet. 2001;10:635-43; Singh LR et al. PLoS Genet. 2010;6:e1000807; Mayfield JA et al. Genetics. 2012;190:1309-23). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.89
BayesDel_addAF	Pathogenic	0.53	D
BayesDel_noAF	Pathogenic	0.52
CADD	Pathogenic	28
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.99	D;D;D;D;.
Eigen	Pathogenic	0.89
Eigen_PC	Pathogenic	0.75
FATHMM_MKL	Uncertain	0.93	D
LIST_S2	Pathogenic	0.99	.;.;.;D;D
M_CAP	Pathogenic	0.66	D
MetaRNN	Pathogenic	0.98	D;D;D;D;D
MetaSVM	Pathogenic	1.1	D
MutationAssessor	Pathogenic	4.2	H;H;H;H;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Uncertain	-2.5	D;D;D;D;D
REVEL	Pathogenic	0.90
Sift	Uncertain	0.012	D;D;D;D;D
Sift4G	Uncertain	0.0050	D;D;D;D;D
Polyphen		1.0	D;D;D;D;.
Vest4		0.89
MutPred		0.93		Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);Loss of sheet (P = 0.0817);
MVP		0.95
MPC		1.1
ClinPred		0.98	D
GERP RS		4.6
Varity_R		0.89
gMVP		0.87

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs121964970; hg19: chr21-44485755;