rs1085308057

Variant names:

• chr2-47475244-A-G
• rs1085308057
• NM_000251.3:c.1979A>G

Your query was ambiguous. Multiple possible variants found:

• chr2-47475244-A-G
• chr2-47475244-A-T

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM1 PM2 PP3_Moderate PP5_Very_Strong

The NM_000251.3(MSH2):​c.1979A>G​(p.Asp660Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: MSH2 NM_000251.3 missense
• Clinical Significance: Likely pathogenic reviewed by expert panel P:2 U:2
• Conservation: PhyloP100: 3.42

Genes affected

MSH2 (HGNC:7325): (mutS homolog 2) This locus is frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). When cloned, it was discovered to be a human homolog of the E. coli mismatch repair gene mutS, consistent with the characteristic alterations in microsatellite sequences (RER+ phenotype) found in HNPCC. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Apr 2012]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PM1: In a region_of_interest Interaction with EXO1 (size 70) in uniprot entity MSH2_HUMAN there are 24 pathogenic changes around while only 4 benign (86%) in NM_000251.3
• PM2: Very rare variant in population databases, with high coverage
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: max_spliceai. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 2-47475244-A-G is Pathogenic according to our data. Variant chr2-47475244-A-G is described in ClinVar as [Likely_pathogenic]. Clinvar id is 427603.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr2-47475244-A-G is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MSH2	NM_000251.3	c.1979A>G	p.Asp660Gly	missense_variant	Exon 12 of 16	ENST00000233146.7	NP_000242.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MSH2	ENST00000233146.7	c.1979A>G	p.Asp660Gly	missense_variant	Exon 12 of 16	1	NM_000251.3	ENSP00000233146.2

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 33

GnomAD4 genome Cov.: 32

ClinVar

Significance: Likely pathogenic

Submissions summary: Pathogenic:2 Uncertain:2

Revision: reviewed by expert panel

Submissions by phenotype

Hereditary cancer-predisposing syndrome Pathogenic:1 Uncertain:1

May 14, 2021

Ambry Genetics

Significance: Pathogenic

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1979A>G intronic pathogenic mutation (also known as p.D660G), located in coding exon 12 of the MSH2 gene, results from an A to G substitution at nucleotide position 1979. The aspartic acid at codon 660 is replaced by glycine, an amino acid with similar properties. This alteration has been detected in several probands whose Lynch syndrome-associated tumors demonstrated high microsatellite instability and/or loss of MSH2 and MSH6 protein expression by immunohistochemistry (Taylor CF et al. Hum. Mutat. 2003 Dec;22:428-33; Sjursen et al. J. Med. Genet. 2010 Sep;47:579-85; Ambry internal data). In a massively parallel cell-based functional assay testing susceptibility to a DNA damaging agent, 6-thioguanine (6-TG), p.D660G was reported to be functionally neutral (Jia X et al. Am J Hum Genet, 2021 01;108:163-175). In addition, RNA studies using patient samples demonstrated that this alteration led to aberrant splicing resulting in an in-frame partial deletion of coding exon 12 (Sjursen et al. J. Med. Genet. 2010 Sep;47:579-85, personal communication with Dr. Sjursen; Ambry internal data). Furthermore, based on an internal structural analysis, this in-frame deletion of nine amino acids is anticipated to result in a significant decrease in structural stability and is in close proximity to the ATP binding site (Warren et al. Molecular Cell 26, 579–592, May 25, 2007; Gupta S et al. Nat Struct Mol Biol, 2011 Dec;19:72-8; Ambry internal data). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). In silico splice site analysis predicts that this alteration will weaken the native splice donor site and will result in the creation or strengthening of a novel splice donor site. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Dec 23, 2018

Color Diagnostics, LLC DBA Color Health

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Lynch syndrome Pathogenic:1

Jun 21, 2019

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Significance: Likely pathogenic

Review Status: reviewed by expert panel

Collection Method: curation

Multifactorial likelihood analysis posterior probability 0.95-0.99 -

Hereditary nonpolyposis colorectal neoplasms Uncertain:1

May 02, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site, but this prediction has not been confirmed by published transcriptional studies. Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The glycine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant has been observed in individuals affected with clinical features of Lynch syndrome (PMID: 14635101, 20587412). ClinVar contains an entry for this variant (Variation ID: 427603). This variant is not present in population databases (ExAC no frequency). This sequence change replaces aspartic acid with glycine at codon 660 of the MSH2 protein (p.Asp660Gly). The aspartic acid residue is moderately conserved and there is a moderate physicochemical difference between aspartic acid and glycine. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.062
BayesDel_addAF	Uncertain	0.069	T
BayesDel_noAF	Benign	-0.14
CADD	Uncertain	25
DANN	Benign	0.97
DEOGEN2	Uncertain	0.46	T;.;.;.
Eigen	Benign	-0.24
Eigen_PC	Benign	0.0062
FATHMM_MKL	Benign	0.75	D
LIST_S2	Benign	0.84	T;T;T;T
M_CAP	Benign	0.023	T
MetaRNN	Benign	0.16	T;T;T;T
MetaSVM	Benign	-0.69	T
MutationAssessor	Benign	0.23	N;.;.;.
PrimateAI	Benign	0.36	T
PROVEAN	Benign	-1.7	N;N;.;N
REVEL	Uncertain	0.32
Sift	Benign	0.41	T;T;.;T
Sift4G	Benign	0.69	T;T;.;T
Polyphen		0.0	B;.;.;B
Vest4		0.37
MutPred		0.43		Loss of ubiquitination at K659 (P = 0.0547);.;Loss of ubiquitination at K659 (P = 0.0547);Loss of ubiquitination at K659 (P = 0.0547);
MVP		0.90
MPC		0.0060
ClinPred		0.57	D
GERP RS		4.8
Varity_R		0.28
gMVP		0.73

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		1.0		Details are displayed if max score is > 0.2
DS_DG_spliceai		1.0		Position offset: -1
DS_DL_spliceai		0.70		Position offset: 26

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

Publications

LitVar

Other links and lift over

dbSNP: rs1085308057; hg19: chr2-47702383;