rs1085308057

chr2-47475244-A-Gchr2-47475244-A-T

Variant summary

Our verdict is Pathogenic. Variant got 11 ACMG points: 12P and 1B. PM1 PM2 PP5_Very_Strong BP4

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 (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. D660E) has been classified as Uncertain significance.

• 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 11 ACMG points.

• PM1: In a hotspot region, there are 3 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 9 benign, 17 uncertain in NM_000251.3
• PM2: Very rare variant in population databases, with high coverage
• 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].
• BP4: Computational evidence support a benign effect (MetaRNN=0.15805867).. Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
MSH2	NM_000251.3	c.1979A>G	p.Asp660Gly	missense_variant	12/16	ENST00000233146.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
MSH2	ENST00000233146.7	c.1979A>G	p.Asp660Gly	missense_variant	12/16	1	NM_000251.3	P1

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

Uncertain significance, criteria provided, single submitter	clinical testing	Color Diagnostics, LLC DBA Color Health	Dec 23, 2018	- -
Pathogenic, criteria provided, single submitter	clinical testing	Ambry Genetics	May 14, 2021	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. -

Lynch syndrome Pathogenic:1

Likely pathogenic, reviewed by expert panel

curation

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Jun 21, 2019

Multifactorial likelihood analysis posterior probability 0.95-0.99 -

Hereditary nonpolyposis colorectal neoplasms Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

May 02, 2019

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;.;.;.
MutationTaster	Benign	0.98	D;D;D
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;