21-43058927-G-A

Variant names:

• chr21-43058927-G-A
• rs28934892
• NM_000071.3:c.1265C>T

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1 PP3_Strong

The NM_000071.3(CBS):​c.1265C>T​(p.Pro422Leu) variant causes a missense change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: CBS NM_000071.3 missense
• Clinical Significance: Uncertain significance criteria provided, multiple submitters, no conflicts P:1 U:6
• Conservation: PhyloP100: 9.46

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 6 ACMG points.

• PM1: In a domain CBS (size 58) in uniprot entity CBS_HUMAN there are 12 pathogenic changes around while only 0 benign (100%) in NM_000071.3
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.982

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBS	NM_000071.3	c.1265C>T	p.Pro422Leu	missense_variant	Exon 14 of 17	ENST00000398165.8	NP_000062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBS	ENST00000398165.8	c.1265C>T	p.Pro422Leu	missense_variant	Exon 14 of 17	1	NM_000071.3	ENSP00000381231.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

TwinsUK AF: 0.00 AC: 0

ALSPAC AF: 0.000259 AC: 1

ClinVar

Significance: Uncertain significance

Submissions summary: Pathogenic:1 Uncertain:6

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Classic homocystinuria Uncertain:3

Uncertain significance, criteria provided, single submitter	clinical testing	Counsyl	Jan 31, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Nov 26, 2018	The CBS c.1265C>T (p.Pro422Leu) variant is a missense variant that has been reported in a compound heterozygous state in at least one individual with a mild form of homocystinuria characterized by high Hcy levels and episodic transient ischemic attacks but no external features or connective tissue disorders characteristic of the disease (Gaustadnes et al. 2010; Maclean et al. 2002). This variant was absent from 100 control alleles and is not reported in the 1000 Genomes Project, Exome Sequencing Project, Exome Aggregation Consortium, or Genome Aggregation Database despite its location of good sequencing coverage. It is therefore presumed to be rare. Functional studies of the variant, which is located in the regulatory domain, conducted in E. coli, CHO-K1 cells, and yeast suggest the p.Pro422Leu variant protein is expressed at the same level as the wild type protein, is thermodynamically stable, and does not show reduced catalytic activity; however, experiments investigating the variant's effect on regulation by S-adenosylmethionine, which is required for in vivo regulation of homocysteine levels, produced conflicting results (Maclean et al. 2002; Kozich et a. 2010; Majtan et al. 2010; Mayfield et al. 2012; Hnízda et al. 2012; Melenovská et al. 2015). The evidence for this variant is limited. The p.Pro422Leu variant is thus classified as of uncertain significance but suspicious for pathogenicity for homocystinuria. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -

HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Sep 17, 2021	This sequence change replaces proline with leucine at codon 422 of the CBS protein (p.Pro422Leu). The proline residue is highly conserved and there is a moderate physicochemical difference between proline and leucine. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individual(s) with homocystinuria (PMID: 12007221). ClinVar contains an entry for this variant (Variation ID: 129). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Possibly Damaging"; Align-GVGD: "Class C0"). Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CBS function (PMID: 12007221, 20506325, 22267502, 22612060, 25331909). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Pathogenic, no assertion criteria provided	literature only	OMIM	Apr 01, 2000	- -

Familial thoracic aortic aneurysm and aortic dissection Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Mar 05, 2020

The p.P422L variant (also known as c.1265C>T), located in coding exon 12 of the CBS gene, results from a C to T substitution at nucleotide position 1265. The proline at codon 422 is replaced by leucine, an amino acid with similar properties. This variant has been reported in at least two individuals with high homocysteine levels, one of whom had history of thrombosis and the other ischemic attacks, but both lacked significant connective tissue findings; these individuals were both compound heterozygotes with a second CBS variant, although phase information was not provided (Gaustadnes M et al. Thromb. Haemost., 2000 Apr;83:554-8; Maclean KN et al. Hum. Mutat., 2002 Jun;19:641-55). Results of functional studies have shown no significant impact on protein expression and stability, but possible differences in protein interactions were suggested in some assays; the clinical impact of these findings is unclear (Maclean KN et al. Hum. Mutat., 2002 Jun;19:641-55; Mayfield JA et al. Genetics, 2012 Apr;190:1309-23; Hnízda A et al. Biochemistry, 2012 06;51:4755-63; Melenovská P et al. J. Inherit. Metab. Dis., 2015 Mar;38:287-94). 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. -

not provided Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

GeneDx

Oct 29, 2020

Not observed in large population cohorts (Lek et al., 2016); 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: 22985361, 22267502, 20490928, 20308073, 19888216, 20506325, 22612060, 12007221, 10780316, 25331909) -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.31
BayesDel_addAF	Pathogenic	0.46	D
BayesDel_noAF	Pathogenic	0.43
CADD	Uncertain	24
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.95	D;D;D;D
Eigen	Uncertain	0.22
Eigen_PC	Benign	0.18
FATHMM_MKL	Pathogenic	0.98	D
LIST_S2	Uncertain	0.89	.;.;.;D
M_CAP	Pathogenic	0.29	D
MetaRNN	Pathogenic	0.98	D;D;D;D
MetaSVM	Benign	-0.39	T
MutationAssessor	Uncertain	2.3	M;M;M;M
PrimateAI	Uncertain	0.63	T
PROVEAN	Pathogenic	-8.4	D;D;D;D
REVEL	Pathogenic	0.77
Sift	Benign	0.072	T;T;T;T
Sift4G	Benign	0.096	T;T;T;T
Polyphen		0.90	P;P;P;P
Vest4		0.98
MutPred		0.82		Loss of phosphorylation at T424 (P = 0.0907);Loss of phosphorylation at T424 (P = 0.0907);Loss of phosphorylation at T424 (P = 0.0907);Loss of phosphorylation at T424 (P = 0.0907);
MVP		0.88
MPC		0.67
ClinPred		0.99	D
GERP RS		4.7
Varity_R		0.76
gMVP		0.79

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: rs28934892; hg19: chr21-44479037; COSMIC: COSV105263805; COSMIC: COSV105263805;