rs28934891

Positions:

• chr21-43058862-C-T

Variant summary

Our verdict is Pathogenic. Variant got 10 ACMG points: 10P and 0B. PM1 PP5_Very_Strong

The ENST00000398165.8(CBS):​c.1330G>A​(p.Asp444Asn) variant causes a missense change involving the alteration of a conserved nucleotide. Variant has been reported in ClinVar as Likely pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. D444D) has been classified as Likely benign.

• Frequency: Genomes: not found (cov: 0)
• Consequence: CBS ENST00000398165.8 missense
• Clinical Significance: Pathogenic/Likely pathogenic criteria provided, multiple submitters, no conflicts P:14
• Conservation: PhyloP100: 7.50

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 Pathogenic. Variant got 10 ACMG points.

• PM1: In a strand (size 5) in uniprot entity CBS_HUMAN there are 5 pathogenic changes around while only 0 benign (100%) in ENST00000398165.8
• PP5: Variant 21-43058862-C-T is Pathogenic according to our data. Variant chr21-43058862-C-T is described in ClinVar as [Likely_pathogenic]. Clinvar id is 126.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-43058862-C-T is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CBS	NM_000071.3	c.1330G>A	p.Asp444Asn	missense_variant	14/17	ENST00000398165.8	NP_000062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CBS	ENST00000398165.8	c.1330G>A	p.Asp444Asn	missense_variant	14/17	1	NM_000071.3	ENSP00000381231	P1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.000334 AC: 56 AN: 167900 Hom.: 0 AF XY: 0.000314 AC XY: 28 AN XY: 89084

Gnomad AFR exome AF: 0.000206

Gnomad AMR exome AF: 0.00131

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: 0.000250

Gnomad OTH exome AF: 0.000649

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.000261 Hom.: 0

TwinsUK AF: 0.000539 AC: 2

ALSPAC AF: 0.00 AC: 0

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000468 AC: 4

ExAC AF: 0.000153 AC: 18

ClinVar

Significance: Pathogenic/Likely pathogenic

Submissions summary: Pathogenic:14

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Classic homocystinuria Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Sep 17, 2017	Across a selection of the available literature, the CBS c.1330G>A (p.Asp444Asn) variant has been identified in at least nine individuals with homocystinuria including four in a homozygous state, three in a compound heterozygous state, and two siblings with the variant in a heterozygous state (Kluijtmans et al. 1996; Kelly et al. 2003; Urreizti et al. 2006; Lefaucheur et al. 2008; Cozar et al. 2011). The variant was also identified in a heterozygous state in the unaffected parents and sister of one of the homozygous individuals (Kluijtmans et al. 1996). The compound heterozygotes all carried a second missense variant on the second allele (Lefaucheur et al. 2008; Cozar et al. 2011). The p.Asp444Asn variant was absent from 80 controls but is reported at a frequency of 0.00134 in the Latino population of the Genome Aggregation Database. Functional studies were performed using cultured fibroblasts from a patient and showed that the p.Asp444Asn variant was not stimulated by physiological levels of S-Adenosylmethionine (AdoMet; a protein which stimulates CBS activity) compared to control fibroblasts, and required increased levels for stimulation (Kluijtmans et al. 1996; Evande et al. 2002). In addition, a study by Hnizda et al. (2012) evaluated protein folding and suggested that C-terminal regulatory domain variants, including the p.Asp444Asn variant, increased protein structural stability and decreased flexibility. Based on the collective evidence, the p.Asp444Asn variant is classified as pathogenic for homocystinuria. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Likely pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Dec 20, 2019	NM_000071.2(CBS):c.1330G>A(D444N) is classified as likely pathogenic in the context of homocystinuria, CBS-related. Sources cited for classification include the following: PMID 22267502, 25331909, 20490928, 16245937, 12269827, 8755636, 12007221, 12552044, 14722927, 14972327, 16479318, 18805305 and 21520339. Classification of NM_000071.2(CBS):c.1330G>A(D444N) is based on the following criteria: This variant has been observed more frequently in patients with clinical diagnoses than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Mar 29, 2024	- -
Likely pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Mar 16, 2022	- -
Likely pathogenic, criteria provided, single submitter	curation	SIB Swiss Institute of Bioinformatics	May 31, 2018	This variant is interpreted as a Likely Pathogenic, for Cystathionine beta-synthase deficiency, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: PS3 => Well-established functional studies show a deleterious effect (PMID:12269827,23974653,20506325,8755636). PM2 => Absent from controls (or at extremely low frequency if recessive; or below the expected carrier frequency if recessive disease or below disease prevalence if dominant disease) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium. PM3 => For recessive disorders, detected in trans with a pathogenic variant (PMID:23974653). PP1 => Cosegregation with disease in multiple affected family members in a gene definitively known to cause the disease (PMID:8755636,). -

not provided Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 10, 2022	Reported in association with classical homocystinuria in patients who harbor additional CBS variants (Maclean et al., 2002; Martinez-Gutierrez et al., 2011; Cozar et al., 2011); Belongs to the class of pathogenic variants in the CBS gene that demonstrate significant residual CBS activity by standard in vitro assays, but impair CBS enzyme function by disruption of proper regulation through SAM activation (Mendes et al., 2014a; Alcaide et al., 2015); Published functional studies demonstrate a damaging effect as this variant disrupts CBS protein interaction with S-adenosylmethionine (also called SAM or AdoMet), a cofactor needed for CBS allosteric activation and protein stability, thus causing reduced CBS protein levels and impairing its ability to be properly activated by physiological levels of SAM (Kluijtmans et al., 1996; Evande et al., 2002; Scott et al., 2004; Prudova et al., 2006; Mendes et al., 2014a; Mendes et al., 2014b; Alcaide et al., 2015); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 8755636, 25044645, 22069143, 18805305, 22267502, 20506325, 16245937, 14722619, 12269827, 16614071, 23974653, 14722927, 12552044, 14972327, 21520339, 16479318, 12007221, 20490928, 25331909, 32768567, 31589614, 33726816, 25218699, 21626167) -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 20, 2013	- -

HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED Pathogenic:2

Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Jan 29, 2024	This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 444 of the CBS protein (p.Asp444Asn). This variant is present in population databases (rs28934891, gnomAD 0.1%). This missense change has been observed in individual(s) with homocystinuria (PMID: 8755636, 14972327, 16479318, 21520339). 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: 126). 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: 8755636, 14722619, 20490928, 20506325, 22069143, 25044645). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Jan 01, 2004	- -

Homocystinuria, pyridoxine-responsive Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 2004

- -

Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1

Likely pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jan 25, 2024

The p.D444N variant (also known as c.1330G>A), located in coding exon 12 of the CBS gene, results from a G to A substitution at nucleotide position 1330. The aspartic acid at codon 444 is replaced by asparagine, an amino acid with highly similar properties. This alteration has been reported in both the compound heterozygous and homozygous states in subjects with pyridoxine responsive homocystinuria (Kluijtmans LA et al. J. Clin. Invest., 1996 Jul;98:285-9; De Lucca M et al. Mol. Genet. Metab., 2004 Mar;81:209-15; Urreizti R et al. J. Hum. Genet., 2006 Feb;51:305-13; Sørensen JT et al. Mol. Genet. Metab., 2016 Mar;117:344-50). Although exhibiting high level of enzyme activity in in vitro assays (Kozich V et al. Hum. Mutat., 2010 Jul;31:809-19; Mayfield JA et al. Genetics, 2012 Apr;190:1309-23; Mendes MI et al. Hum. Mutat., 2014 Oct;35:1195-202), this alteration has been reported to render the mutant protein unresponsive to the allosteric regulator S-adenosylmethionine, which could subsequently affect protein stability and function (Kluijtmans LA et al. J. Clin. Invest., 1996 Jul;98:285-9; Evande R et al. Biochemistry, 2002 Oct;41:11832-7; Scott JW et al. J. Clin. Invest., 2004 Jan;113:274-84; Mendes MI et al. Hum. Mutat., 2014 Oct;35:1195-202). This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Based on the majority of available evidence to date, this variant is likely to be pathogenic. -

CBS-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Sep 17, 2024

The CBS c.1330G>A variant is predicted to result in the amino acid substitution p.Asp444Asn. This variant has been reported to be causative for homocystinuria (Kluijtmans et al. 1999. PubMed ID: 10364517; Cozar et al. 2011. PubMed ID: 21520339). This variant is reported in 0.13% of alleles in individuals of Latino descent in gnomAD (http://gnomad.broadinstitute.org/variant/21-44478972-C-T). This variant is interpreted as pathogenic. -

Homocystinuria Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

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

Oct 30, 2017

Variant summary: The CBS c.1330G>A (p.Asp444Asn) variant involves the alteration of a conserved nucleotide that lies within the CBS domain (InterPro). 3/4 in silico tools predict a benign outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 65/192534 control chromosomes at a frequency of 0.0003376, which does not exceed the estimated maximal expected allele frequency of a pathogenic CBS variant (0.0030414). The variant has been reported in numerous patients with CBS-related homocystinuria, including homozygous patients. Functional studies suggest that CBS expression and activity levels are similar to those found in heterozygous individuals, but binding with the necessary cofactor S-adenosylmethionine and the subsequent induction of CBS protein activity is impaired (Mendes_2013). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.43
BayesDel_addAF	Benign	-0.20	T
BayesDel_noAF	Benign	-0.090
CADD	Pathogenic	26
DANN	Pathogenic	1.0
DEOGEN2	Pathogenic	0.93	D;D;D;D
Eigen	Uncertain	0.38
Eigen_PC	Uncertain	0.42
FATHMM_MKL	Uncertain	0.86	D
LIST_S2	Uncertain	0.96	.;.;.;D
M_CAP	Uncertain	0.21	D
MetaRNN	Uncertain	0.59	D;D;D;D
MetaSVM	Benign	-0.29	T
MutationAssessor	Uncertain	2.3	M;M;M;M
MutationTaster	Benign	1.0	A;A;A;A;A;A;A;A;A;A;A;A
PrimateAI	Uncertain	0.62	T
PROVEAN	Uncertain	-3.1	D;D;D;D
REVEL	Uncertain	0.60
Sift	Benign	0.10	T;T;T;T
Sift4G	Benign	0.14	T;T;T;T
Polyphen		0.12	B;B;B;B
Vest4		0.93
MVP		0.90
MPC		0.42
ClinPred		0.14	T
GERP RS		4.7
Varity_R		0.75
gMVP		0.79

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs28934891; hg19: chr21-44478972;