rs121964962
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Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PP3_StrongPP5_Very_Strong
The NM_000071.3(CBS):c.919G>A(p.Gly307Ser) variant causes a missense change. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★).
Frequency
Genomes: not found (cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CBS
NM_000071.3 missense
NM_000071.3 missense
Scores
12
6
1
Clinical Significance
Conservation
PhyloP100: 6.85
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]
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ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 12 ACMG points.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.971
PP5
Variant 21-43062988-C-T is Pathogenic according to our data. Variant chr21-43062988-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 117.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-43062988-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.919G>A | p.Gly307Ser | missense_variant | 10/17 | ENST00000398165.8 | NP_000062.1 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| CBS | ENST00000398165.8 | c.919G>A | p.Gly307Ser | missense_variant | 10/17 | 1 | NM_000071.3 | ENSP00000381231 | P1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
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0
GnomAD3 exomes AF: 0.000155 AC: 39AN: 251400Hom.: 0 AF XY: 0.000169 AC XY: 23AN XY: 135886
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GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 46Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 26
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Data not reliable, filtered out with message: AC0;AS_VQSR
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ESP6500AA
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:17Other:1
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Classic homocystinuria Pathogenic:8Other:1
| Pathogenic, no assertion criteria provided | clinical testing | Child Health and Human Development Program, Research Institute of the McGill University Health Center | - | The c.919G>A (G307S) was identified in a patient of African & French Canadian origin in compound heterozygote with c.941G>C (V314A). Clinical characteristics included lens dislocation and elevated fasting homocysteine. Patient had a mild intellectual impairment and does not respond to treatment with vitamin B6. - |
| Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | Mar 28, 2024 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Apr 27, 2017 | The CBS c.919G>A (p.Gly307Ser) variant is well described as a common pathogenic allele in individuals with homocystinuria of Celtic origin, accounting for 71% of disease associated alleles in Ireland, 21% in the UK and 8% in the US (Moat et al. 2004). The presence of a single allele almost always predicts non-responsiveness to pyroxidine therapy. The p.Gly307Ser variant has been reported in at least six studies in which it is found in a total of 44 individuals including 14 in a homozygous state (including two pairs of siblings), ten in a compound heterozygous state (four of whom were related), and 20 heterozygotes in whom a second allele has not yet been identified (Hu et al. 1993; Gallagher et al. 1995; Kim et al. 1997; Kelly et al. 2003; Moat et al. 2004; Stabler et al. 2013). The variant was also found in at least three unaffected heterozygous relatives. The variant was absent from 82 control chromosomes but is reported at a frequency of 0.00026 in the European (non-Finnish) population of the Exome Aggregation Consortium. Functional studies have demonstrated that the Gly307 residue is located in the catalytic site of the protein and results in the production of correctly assembled tetramers that are slightly unfolded with a shift towards unfolded intermediates. The catalytic activity of the p.Gly307Ser variant protein is completely abolished (Hu et al. 1993; Hnizda et al. 2012). Based on the collective evidence, the p.Gly307Ser variant is classified as pathogenic for homocystinuria. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. - |
| not provided, no classification provided | literature only | GeneReviews | - | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Nov 12, 2019 | NM_000071.2(CBS):c.919G>A(G307S) is classified as pathogenic in the context of CBS-related homocystinuria, and is associated with the B6-non-responsive form of this disease. Sources cited for classification include the following: PMID 9889017, 20506325, 7506602 and 22267502. Classification of NM_000071.2(CBS):c.919G>A(G307S) is based on the following criteria: This is a well-established pathogenic variant in the literature that 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 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Genetics and Molecular Pathology, SA Pathology | Nov 05, 2021 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Apr 04, 2022 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 08, 2019 | The p.Gly307Ser variant in CBS has been reported in at least 11 homozygous, 4 compound heterozygous and 15 heterozygous (where the second variant has not been reported) probands with homocystinuria and segregated with disease in 5 affected family members (Hu 1993, Dawson 1996, Stabler 2013, Gallagher 1995, Moat 2004). It was also reported in 1 heterozygous individual with homocystinuria and reversible cerebral white matter abnormalities who was also heterozygous for the MTHFR c.677C>T variant (Ismayilova 2019). This variant has been reported in ClinVar (ClinVar ID 117). In addition, in vitro functional studies provide evidence that the variant leads to impaired protein function (Hu 1993, Hnizda 2012, Kozich 2010, Mayfield 2012). This variant has also been identified in 41/129158 of European chromosomes by gnomAD (http://gnomad.broadinstitute.org/). However, this frequency is low enough to be consistent with a recessive carrier frequency. In summary, this variant meets criteria to be classified as pathogenic for autosomal recessive homocystinuria. ACMG/AMP Criteria applied: PM3_very_strong, PP1_strong, PS3_supporting. - |
not provided Pathogenic:3
| Pathogenic, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Nov 20, 2014 | - - |
| Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | May 01, 2024 | CBS: PM3:Very Strong, PM2, PP3, PP4, PS3:Supporting - |
| Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Nov 05, 2019 | Common pathogenic variant found on approximately 70% of alleles in patients of Celtic origin with homocystinuria due to cystathionine beta-synthase (CBS) deficiency and is usually associated with a more severe non-B6 responsive phenotype (Urreizti et al., 2006); Functional studies found that G307S is associated with significantly decreased CBS enzyme activity compared to wild-type (Hu et al. 1993; Kozich et al. 2010; Hnizda et al. 2012); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 25087612, 7581402, 14722927, 7564249, 17319270, 12552044, 8744616, 22267502, 23733603, 22069143, 7506602, 16479318, 30609409, 30187370, 12686134, 18280597, 12124992, 9361025, 25636110, 20506325) - |
HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED Pathogenic:2
| Pathogenic, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 21, 2024 | This sequence change replaces glycine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 307 of the CBS protein (p.Gly307Ser). This variant is present in population databases (rs121964962, gnomAD 0.03%). This missense change has been observed in individual(s) with homocystinuria (PMID: 7506602, 7581402, 8744616, 9889017, 23733603). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 117). 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: 20506325, 22267502). For these reasons, this variant has been classified as Pathogenic. - |
| Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 28, 2003 | - - |
Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1
| Pathogenic, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2023 | The p.G307S pathogenic mutation (also known as c.919G>A), located in coding exon 8 of the CBS gene, results from a G to A substitution at nucleotide position 919. The glycine at codon 307 is replaced by serine, an amino acid with similar properties. This alteration was described to account for about 70% of disease alleles in Ireland (Gallagher PM et al. Hum. Mutat., 1995;6:177-80), 21% in UK and 8% in US (Moat SJ et al. Hum. Mutat., 2004 Feb;23:206). This alteration has been reported in the homozygous state in multiple individuals with homocysteinuria, as well as in the heterozygous state in patients with an (un)identified second allele (Dawson PA et al. Aust N Z J Med, 1996 Apr;26:180-5; Gallagher PM et al. Hum. Mutat., 1995;6:177-80; Kim CE et al. Hum. Mol. Genet., 1997 Dec;6:2213-21; Moat SJ et al. Hum. Mutat., 2004 Feb;23:206). In addition, this alteration was reported to occur in the enzyme active site (Meier M et al. Biochim. Biophys. Acta, 2003 Apr;1647:206-13), and in vitro studies have consistently suggested that this change would abolish enzyme activity, probably by interfering with protein folding (Kim CE et al. Hum. Mol. Genet., 1997 Dec;6:2213-21; Kozich V et al. Hum. Mutat., 2010 Jul;31:809-19; Mayfield JA et al. Genetics, 2012 Apr;190:1309-23; Hnízda A et al. J. Inherit. Metab. Dis., 2012 May;35:469-77). In addition, this alteration is predicted to be deleterious by BayesDel in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. - |
Homocystinuria, pyridoxine-nonresponsive Pathogenic:1
| Pathogenic, no assertion criteria provided | literature only | OMIM | Jan 28, 2003 | - - |
CBS-related disorder Pathogenic:1
| Pathogenic, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | May 17, 2024 | The CBS c.919G>A variant is predicted to result in the amino acid substitution p.Gly307Ser. This variant is one of the most commonly reported CBS variants causative for homocystinuria due to cystathionine beta-synthase deficiency (e.g., Gallagher et al. 1995. PubMed ID: 7581402; Kraus et al. 1999. PubMed ID: 10338090). In experimental studies, the p.Gly307Ser substitution has been shown to greatly impair CBS enzyme activity (Kozich et al. 2010. PubMed ID: 20506325; Mayfield et al. 2012. PubMed ID: 22267502). This variant is reported in 0.032% of alleles in individuals of European (Non-Finnish) descent in gnomAD. 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 | Apr 06, 2017 | Variant summary: The CBS c.919G>A (p.Gly307Ser) variant involves the alteration of a conserved nucleotide. 5/5 in silico tools predict a damaging outcome for this variant. This variant was found in 19/121292 control chromosomes at a frequency of 0.0001566, which does not exceed the estimated maximal expected allele frequency of a pathogenic CBS variant (0.0030414). This variant has been reported in many affected individuals and functional study showed variant with <1% activity in comparison with WT (Kozich_2010). In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as pathogenic. Taken together, this variant is classified as pathogenic. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D;D;D;D
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Pathogenic
.;.;.;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D
MetaSVM
Pathogenic
D
MutationAssessor
Pathogenic
M;M;M;M
MutationTaster
Benign
A;A;A;A;A;A;A;A;A;A;A;A
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D;D
REVEL
Pathogenic
Sift
Uncertain
D;D;D;D
Sift4G
Uncertain
D;D;D;D
Polyphen
D;D;D;D
Vest4
MVP
MPC
1.1
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at