rs117687681

Positions:

chr21-43060481-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 5P and 4B. PM1PM5PP3BP4_ModerateBS1_SupportingBS2_Supporting

The NM_000071.3(CBS):c.1105C>T(p.Arg369Cys) variant causes a missense change. In-silico tool predicts a benign 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. R369H) has been classified as Pathogenic.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0043 ( 5 hom. )

Failed GnomAD Quality Control

Consequence

CBS
NM_000071.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:17B:1O:1

Conservation

PhyloP100: 6.40

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 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 NM_000071.3

PM5

Other missense variant is known to change same aminoacid residue: Variant chr21-43060480-C-T is described in Lovd as [Pathogenic].

PP3

Multiple lines of computational evidence support a deleterious effect 8: BayesDel_addAF, BayesDel_noAF, Cadd, Dann, Eigen, M_CAP, PROVEAN, REVEL [when AlphaMissense, max_spliceai, FATHMM_MKL, MetaRNN, MutationTaster was below the threshold]

BP4

Computational evidence support a benign effect (MetaRNN=0.14451393).

BS1

Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.00426 (180/42276) while in subpopulation MID AF= 0.00595 (1/168). AF 95% confidence interval is 0.00509. There are 5 homozygotes in gnomad4_exome. There are 83 alleles in male gnomad4_exome subpopulation. Median coverage is 0. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting

BS2

High Homozygotes in GnomAdExome4 at 5 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/exons	MANE	Protein	UniProt
CBS	NM_000071.3 link	c.1105C>T	p.Arg369Cys	missense_variant	12/17	ENST00000398165.8	NP_000062.1	P35520-1Q9NTF0

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CBS	ENST00000398165.8 link	c.1105C>T	p.Arg369Cys	missense_variant	12/17	1	NM_000071.3	ENSP00000381231.4		P35520-1

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad NFE

AF:

0.00

GnomAD3 exomes

AF:

0.00307

AC:

758

AN:

246960

Hom.:

AF XY:

0.00296

AC XY:

398

AN XY:

134310

show subpopulations

Gnomad AFR exome

AF:

0.00125

Gnomad AMR exome

AF:

0.00148

Gnomad ASJ exome

AF:

0.00689

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00226

Gnomad NFE exome

AF:

0.00495

Gnomad OTH exome

AF:

0.00329

GnomAD4 exome

AF:

0.00426

AC:

180

AN:

42276

Hom.:

Cov.:

AF XY:

0.00367

AC XY:

AN XY:

22632

show subpopulations

Gnomad4 AFR exome

AF:

0.00167

Gnomad4 AMR exome

AF:

0.00355

Gnomad4 ASJ exome

AF:

0.0126

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00487

Gnomad4 NFE exome

AF:

0.00591

Gnomad4 OTH exome

AF:

0.00643

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

Alfa

AF:

0.00426

Hom.:

TwinsUK

AF:

0.00431

AC:

ALSPAC

AF:

0.00337

AC:

ESP6500AA

AF:

0.00113

AC:

ESP6500EA

AF:

0.00395

AC:

ExAC

AF:

0.00323

AC:

392

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00425

EpiControl

AF:

0.00415

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:17Benign:1Other:1

Revision: criteria provided, conflicting classifications

LINK: link

Submissions by phenotype

Classic homocystinuria

Uncertain:7

Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 27, 2017	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. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mendelics	May 28, 2019	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	Jun 11, 2020	Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as 3B-VUS. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. (N) 0106 - This gene is known to be associated with autosomal recessive disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from arginine to cysteine (exon 12). (N) 0251 - Variant is heterozygous. (N) 0304 - Variant is present in gnomAD <0.01 for a recessive condition (838 heterozygotes, 5 homozygotes). (P) 0309 - An alternative amino acid change at the same position has been observed in gnomAD (4 heterozygotes, 0 homozygotes). (N) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (P) 0600 - Variant is located in an annotated domain or motif. This variant is located within the active core (PMID: 30380942) in the PALP domain (PDB, Decipher) (N) 0708 - Comparable variants have conflicting previous evidence for pathogenicity. A different variant in the same codon resulting in a change to a histidine has also been reported as VUS in a patient with homocystinuria (ClinVar). Functional studies showed that a change to proline (not seen in patients) was shown to result in a phenotype on yeast, whereas the change to histidine did not (PMID: 22267502). (N) 0808 - Previous reports of pathogenicity are conflicting. This variant has been previously reported as VUS in individuals with homocystinuria. (ClinVar, PMID: 29650765). (N) 1002 - Functional evidence is conflicting. Studies in different systems, such as yeast and mammals cells showed discrepant results in protein folding and enzyme activity (PMID: 9361025, PMID: 18950795). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign -
Uncertain significance, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Mar 29, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center	Apr 04, 2024	- -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Jan 12, 2020	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genome-Nilou Lab	May 18, 2021	- -

not provided

Uncertain:5Benign:1Other:1

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Jul 22, 2024	Multiple in vitro functional analyses of this variant in various expression systems have yielded inconsistent conclusions regarding pathogenicity (PMID: 18950795, 20506325, 22069143, 22267502); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Identified in association with neural tube defects (NTD) in published literature (PMID: 29205322, 31139930); This variant is associated with the following publications: (PMID: 20981092, 10364517, 10338090, 20506325, 12124992, 9361025, 25087612, 22267502, 18950795, 15319318, 15192637, 22069143, 29650765, 22612060, 34426522, 26990548, 19819175, 28152038, 25331909, 34074348, Sharo2022[Preprint], 36588553, 36385415, 32245022, 31301157, 30165906, 18708589, 29205322, 31139930) -
Likely benign, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jun 01, 2024	CBS: PS3:Supporting, BS2 -
Uncertain significance, criteria provided, single submitter	clinical testing	Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	Jun 15, 2017	- -
not provided, no classification provided	phenotyping only	GenomeConnect, ClinGen	-	GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -
Uncertain significance, criteria provided, single submitter	clinical testing	Mayo Clinic Laboratories, Mayo Clinic	May 10, 2023	PP3 -
Uncertain significance, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Nov 20, 2015	- -
Uncertain significance, criteria provided, single submitter	clinical testing	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	Nov 16, 2023	The CBS c.1105C>T; p.Arg369Cys variant (rs117687681) is reported in the literature in individuals affected with homocystinuria, several of whom carried an additional pathogenic variant (Kim 1997, Gaustadnes 2002, Kluijtmans 1999). However, this variant is also found in the general population with an overall allele frequency of 0.3% (838/278330 alleles, including 5 homozygotes) in the Genome Aggregation Database. The arginine at codon 369 is highly conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.972). Functional studies present conflicting results, with in vitro analyses suggesting reduced enzyme activity (Hnizda 2012, Kozich 2010), while complementation studies in yeast indicate function comparable to wildtype (Kim 1997, Mayfield 2012). Due to conflicting information, the clinical significance of the p.Arg369Cys variant is uncertain at this time. References: Gaustadnes M et al. The molecular basis of cystathionine beta-synthase deficiency in Australian patients: genotype-phenotype correlations and response to treatment. Hum Mutat. 2002 Aug;20(2):117-26. PMID: 12124992. Hnizda A et al. Cystathionine beta-synthase mutants exhibit changes in protein unfolding: conformational analysis of misfolded variants in crude cell extracts. J Innherit Metab dis 2012; 35:469-477. PMID: 22069143. Kim et al. Functional modeling of vitamin responsiveness in yeast: a common pyridoxine-responsive cystathionine beta-synthase mutation in homocystinuria. Hum Mol Genet. 1997; 6(13): 2213-2221. PMID: 9361025. Kluijtmans et al. The molecular basis of cystathionine beta-synthase deficiency in Dutch patients with homocystinuria: effect of CBS genotype on biochemical and clinical phenotype and on response to treatment. Am J Hum Genet. 1999 Jul;65(1):59-67. PMID: 10364517. Kozich V et al. Cystathionine beta-synthase mutations: effect of mutation topology on folding and activity. Hum Mutat 2010; 31(7):809-819. PMID: 20506325. Mayfield JA et al. Surrogate genetics and metabolic profiling for characterization of human disease alleles. Genetics 2012; 190:1309-1323. PMID: 22267502. -

not specified

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

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

Aug 06, 2024

Variant summary: CBS c.1105C>T (p.Arg369Cys) results in a non-conservative amino acid change located in the Tryptophan synthase beta chain-like, PALP domain (IPR001926) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.003 in 278330 control chromosomes, predominantly at a frequency of 0.0048 within the Non-Finnish European subpopulation in the gnomAD database, including 4 homozygotes. The observed variant frequency within Non-Finnish European control individuals in the gnomAD database is approximately 1.58 fold of the estimated maximal expected allele frequency for a pathogenic variant in CBS causing Homocystinuria phenotype (0.003). c.1105C>T has been reported in the literature in individuals affected with Cystathionine beta synthase deficiency (CBSD) (e.g. Kim_1997, Kluijtmans_1999, Gaustadnes_2002, Janosick_2009). In one patient, this variant co-occurred in cis with another potentially pathogenic missence variant resulting in a complete loss of enzymatic activity and a severe disease phenotype (Kluijtmans_1999). However, the sole contribution of this variant to the associated pathophysiology could not be determined. Additionally, other possible causes of homocyctinurea, such as mutations in MTHFR, MTR, MTRR and MMADHC genes have not been ruled out. Homozygotes for this R369C are B6-responsive in a corrective dose of a daily multivitamins and presented with a mild phenotype or no symptoms. This may explain the high frequency of this variant in gnomAD database. The functional studies displayed discordant results when tested in the different expression systems. However, in all functional studies cells harboring the R369C showed moderately reduced activity and lower rate of a tetramer formation (active form) (Kim_1997, Janosick_2009, Kozich_2010, Mayfield_2012). The following publications have been ascertained in the context of this evaluation (PMID: 32245022, 30165906, 12124992, 22612060, 29205322, 18708589, 18950795, 29650765, 31301157, 9361025, 10364517, 20506325, 28152038, 22267502, 31664448, 25331909, 31139930, 19819175, 31211624, 36588553). ClinVar contains an entry for this variant (Variation ID: 212860). Based on the evidence outlined above, the variant was classified as VUS-possibly benign. -

Familial thoracic aortic aneurysm and aortic dissection

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

May 26, 2023

The p.R369C variant (also known as c.1105C>T), located in coding exon 10 of the CBS gene, results from a C to T substitution at nucleotide position 1105. The arginine at codon 369 is replaced by cysteine, an amino acid with highly dissimilar properties. This variant has been reported in several individuals and cohorts with homocystinuria who were B6 responsive (Kim CE et al. Hum. Mol. Genet., 1997 Dec;6:2213-21; Gaustadnes M et al. Hum. Mutat., 2002 Aug;20:117-26). Newborn blood screening found this variant to be present at a frequency of approximately 0.8% and 0.5% in Norway and Czech, respectively (Refsum H et al. J. Pediatr., 2004 Jun;144:830-2; Janosík M et al. J. Pediatr., 2009 Mar;154:431-7). This variant was reported not to affect yeast growth (Kim CE et al. Hum. Mol. Genet., 1997 Dec;6:2213-21), but attenuated enzyme activity in E. coli and CHO-K1 cells to some extent (Janosík M et al. J. Pediatr., 2009 Mar;154:431-7). Based on data from gnomAD, the frequency for this variant is above the maximum credible frequency for a disease-causing variant in this gene based on internally established thresholds (Karczewski et al. Nature. 2020 May;581(7809):434-443; Whiffin et al. Genet Med. 2017 10;19:1151-1158). 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. -

HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Nov 01, 2022

This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 369 of the CBS protein (p.Arg369Cys). This variant is present in population databases (rs117687681, gnomAD 0.7%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with pyridoxine-responsive homocystinuria (PMID: 9361025, 10364517, 12124992, 18950795). 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: 212860). 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. Experimental studies have shown that this missense change affects CBS function (PMID: 10364517, 18708589, 18950795, 20506325). 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. -

Connective tissue disorder

Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Genome Diagnostics Laboratory, The Hospital for Sick Children

Nov 16, 2021

- -

CBS-related disorder

Uncertain:1

Uncertain significance, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Dec 15, 2023

The CBS c.1105C>T variant is predicted to result in the amino acid substitution p.Arg369Cys. This variant has been reported in the compound heterozygous state along with a second pathogenic variant in two individuals with CBS deficiency. Both of these patients were reported to be pyridoxine responsive with clinical presentations that ranged from asymptomatic to severe psychiatric disturbances (Kim et al. 1997. PubMed ID: 9361025; Gaustadnes et al. 2002. PubMed ID: 12124992). It has also been reported in the homozygous state in a patient with CBS deficiency, although that patient was also homozygous for a second missense variant in CBS (p.Arg491Cys; Kluijtmans et al. 1999. PubMed ID: 10364517). In addition, it was more recently reported with a second rare missense variant in CBS in a patient without clinical or biochemical features of homocystinuria. No additional segregation studies were performed for that patient (Kaadan et al. 2018. PubMed ID: 29650765). The c.1105C>T variant has been reported to be one of the most common CBS variants among Northern Europeans (Refsum et al. 2004. PubMed ID: 15192637; Janosík et al. 2009. PubMed ID: 18950795). Consistent with these reports, the c.1105C>T variant is listed in the gnomAD database at an allele frequency of ~0.5% in the European population, and 4 homozygotes are reported in this population group. In vitro functional studies have shown that the p.Arg369Cys change leads to a decrease in CBS activity relative to wild-type in E. coli and mammalian (CHO cells) expression systems, as well decreasing protein stability (Janosík et al. 2009. PubMed ID: 18950795; Kozich et al. 2010. PubMed ID: 20506325; Hnízda et al. 2012. PubMed ID: 22069143; Melenovská et al. 2015. PubMed ID: 25331909), although the p.Arg369Cys substitution seems to have no deleterious effect in a yeast expression system (Mayfield et al. 2012. PubMed ID: 22267502). Lastly, we have observed this variant internally in many individuals, some of whom had positive test results in other genes that explained their phenotype, and the majority of which had no second CBS variant identified. One patient was homozygous for the c.1105C>T variant and had some clinical features that could be consistent with CBS deficiency. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.15

BayesDel_addAF

Pathogenic

0.21

BayesDel_noAF

Pathogenic

0.53

CADD

Pathogenic

DANN

Pathogenic

1.0

DEOGEN2

Pathogenic

0.99

D;D;D;D

Eigen

Pathogenic

0.79

Eigen_PC

Pathogenic

0.72

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Pathogenic

0.99

.;.;.;D

M_CAP

Pathogenic

0.80

MetaRNN

Benign

0.14

T;T;T;T

MetaSVM

Pathogenic

1.1

MutationAssessor

Uncertain

2.3

M;M;M;M

PrimateAI

Uncertain

0.60

PROVEAN

Pathogenic

-6.2

D;D;D;D

REVEL

Pathogenic

0.97

Sift

Uncertain

0.0040

D;D;D;D

Sift4G

Uncertain

0.0060

D;D;D;D

Polyphen

1.0

D;D;D;D

Vest4

0.92

MVP

0.93

MPC

1.3

ClinPred

0.029

GERP RS

4.9

Varity_R

0.84

gMVP

0.88

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

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

Other links and lift over