rs63751711

Variant names:

• chr3-37012099-G-A
• rs63751711
• NM_000249.4:c.677G>A

Your query was ambiguous. Multiple possible variants found:

• chr3-37012099-G-A
• chr3-37012099-G-T
• chr3-37012099-G-C

Variant summary

Our verdict is Pathogenic. The variant received 20 ACMG points: 20P and 0B. PS3 PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.677G>A​(p.Arg226Gln) variant causes a missense, splice region change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000689 in 1,452,078 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★★). ClinVar reports functional evidence for this variant: "SCV005427849: RNA studies (PMID:9777949, 18561205)." and additional evidence is available in ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Pathogenic in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R226L) has been classified as Likely pathogenic. The gene MLH1 is included in the ClinGen Criteria Specification Registry.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 6.9e-7 (0 hom.)
• Consequence: MLH1 NM_000249.4 missense, splice_region
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic reviewed by expert panel P:23
• Conservation: PhyloP100: 7.59
• Publications: 58 publications found

Genes affected

MLH1 (HGNC:7127): (mutL homolog 1) The protein encoded by this gene can heterodimerize with mismatch repair endonuclease PMS2 to form MutL alpha, part of the DNA mismatch repair system. When MutL alpha is bound by MutS beta and some accessory proteins, the PMS2 subunit of MutL alpha introduces a single-strand break near DNA mismatches, providing an entry point for exonuclease degradation. The encoded protein is also involved in DNA damage signaling and can heterodimerize with DNA mismatch repair protein MLH3 to form MutL gamma, which is involved in meiosis. This gene was identified as a locus frequently mutated in hereditary nonpolyposis colon cancer (HNPCC). [provided by RefSeq, Aug 2017]

MLH1 Gene-Disease associations (from GenCC):

• Lynch syndrome

  Inheritance: AD Classification: DEFINITIVE, SUPPORTIVE Submitted by: ClinGen, Orphanet, G2P
• Lynch syndrome 2

  Inheritance: AD Classification: DEFINITIVE, STRONG Submitted by: Ambry Genetics, Genomics England PanelApp
• Muir-Torre syndrome

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Genomics England PanelApp, Ambry Genetics, G2P, Orphanet
• mismatch repair cancer syndrome 1

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Ambry Genetics, G2P, ClinGen
• Lynch syndrome 1

  Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• ovarian cancer

  Inheritance: AD Classification: STRONG Submitted by: Genomics England PanelApp
• malignant pancreatic neoplasm

  Inheritance: AD Classification: MODERATE Submitted by: Genomics England PanelApp
• rhabdomyosarcoma

  Inheritance: AR Classification: MODERATE Submitted by: Genomics England PanelApp
• prostate cancer

  Inheritance: AD Classification: LIMITED Submitted by: Ambry Genetics
• breast cancer

  Inheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
• hereditary breast carcinoma

  Inheritance: AD Classification: NO_KNOWN Submitted by: ClinGen

ACMG classification

Specifications for MLH1 are available in the ClinGen Criteria Specification Registry and recommended for reference when assigning criteria.

Our verdict: Pathogenic. The variant received 20 ACMG points.

• PS3: PS3 evidence extracted from ClinVar submissions: SCV005427849: RNA studies (PMID: 9777949, 18561205).; SCV000187278: RNA studies have demonstrated that this alteration results in abnormal splicing in the set of samples tested (Ambry internal data).; SCV000684857: RNA studies with carrier individuals have shown that this variant cause an out-of-frame skipping of exon 8 (PMID:18561205) and exons 8-10 (PMID: 21034533).; SCV005901679: These results have been confirmed in a minigene assay (PMID: 15300854, 16341550, 18561205); SCV000321896: "Protein and RNA-based functional studies show that this variant disrupts the adjacent natural splice donor site leading to skipping of exon 8, resulting in a frameshift." PMID: 9777949, 15300854, 16341550, 18561205; SCV000601408: This variant has been described as pathogenic and/or having a deleterious effect on MLH1 protein function in the published literature by compromising normal splicing and resulting in the skipping of exon 8 (PMID: 15300854 (2004), 16341550 (2006), and 18561205 (2008)).; SCV001549017: "The variant is detected in Exon 8 at donor site of the intron, localized in the splice junction and is predicted to cause abnormal splicing. RNA analysis with a primer localized in exon 8, have shown that this substitution results in a complete loss of exon 8 (Pagenstecher 2006, Sharp 2004, Tournier 2008)."; SCV004018169: Functional studies indicate this variant impacts protein function [PMID:16341550].; SCV000284072: Studies have shown that this missense change results in skipping of exon 8, and produces a non-functional protein and/or introduces a premature termination codon (PMID: 15300854, 16341550, 18561205, 21034533; internal data).; SCV000917644: "These predictions were also confirmed by functional studies, showing that the variant which is located at the last nucleotide of exon 8, disrupts the splice donor site and leads to skipping of exon 8, resulting in a frameshift with a consequential stop codon (Sharp 2004, Pagenstecher 2006, Tournier2008)."
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-37012099-G-T is described in ClinVar as Likely_pathogenic. ClinVar VariationId is 90319.Status of the report is reviewed_by_expert_panel, 3 stars.
• PP3: Splicing predictors support a deleterious effect. Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. Scorers claiming Uncertain: max_spliceai. No scorers claiming Benign.
• PP5: Variant 3-37012099-G-A is Pathogenic according to our data. Variant chr3-37012099-G-A is described in ClinVar as Pathogenic. ClinVar VariationId is 90318.Status of the report is reviewed_by_expert_panel, 3 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_000249.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	NM_000249.4	MANE Select	c.677G>A	p.Arg226Gln	missense splice_region	Exon 8 of 19	NP_000240.1	P40692-1
	MLH1	NM_001354628.2		c.677G>A	p.Arg226Gln	missense splice_region	Exon 8 of 18	NP_001341557.1	A0A087WX20
	MLH1	NM_001354629.2		c.578G>A	p.Arg193Gln	missense splice_region	Exon 7 of 18	NP_001341558.1	A0AAQ5BGZ2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	MLH1	ENST00000231790.8	TSL:1 MANE Select	c.677G>A	p.Arg226Gln	missense splice_region	Exon 8 of 19	ENSP00000231790.3	P40692-1
	MLH1	ENST00000456676.7	TSL:1	c.677G>A	p.Arg226Gln	missense splice_region	Exon 8 of 17	ENSP00000416687.3	H0Y818
	MLH1	ENST00000413740.2	TSL:1	c.677G>A	p.Arg226Gln	missense splice_region	Exon 8 of 15	ENSP00000416476.2	H0Y806

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 6.89e-7 AC: 1 AN: 1452078 Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0 AN XY: 722968

African (AFR) AF: 0.00 AC: 0 AN: 33350

American (AMR) AF: 0.00 AC: 0 AN: 44714

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 26088

East Asian (EAS) AF: 0.00 AC: 0 AN: 39670

South Asian (SAS) AF: 0.00 AC: 0 AN: 86126

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 53390

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 5752

European-Non Finnish (NFE) AF: 9.07e-7 AC: 1 AN: 1102856

Other (OTH) AF: 0.00 AC: 0 AN: 60132

GnomAD4 genome Cov.: 32

Alfa AF: 0.0000478 Hom.: 0

Bravo AF: 0.00000756

ClinVar

ClinVar submissions

Significance: Pathogenic

Revision: reviewed by expert panel

Pathogenic	VUS	Benign	Condition
6	-	-	not provided (6)
4	-	-	Hereditary cancer-predisposing syndrome (4)
4	-	-	Lynch syndrome (4)
3	-	-	Colorectal cancer, hereditary nonpolyposis, type 2 (3)
1	-	-	Endometrial carcinoma (1)
1	-	-	Gastric cancer (1)
1	-	-	Hereditary nonpolyposis colon cancer (1)
1	-	-	Hereditary nonpolyposis colorectal neoplasms (1)
1	-	-	Lynch syndrome 1 (1)
1	-	-	Lynch-like syndrome (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.30
BayesDel_addAF	Pathogenic	0.43	D
BayesDel_noAF	Pathogenic	0.38
CADD	Pathogenic	35
DANN	Pathogenic	1.0
DEOGEN2	Uncertain	0.60	D
Eigen	Pathogenic	0.78
Eigen_PC	Pathogenic	0.81
FATHMM_MKL	Pathogenic	1.0	D
LIST_S2	Uncertain	0.97	D
M_CAP	Pathogenic	0.31	D
MetaRNN	Pathogenic	0.80	D
MetaSVM	Uncertain	0.67	D
MutationAssessor	Benign	1.6	L
PhyloP100		7.6
PrimateAI	Uncertain	0.54	T
PROVEAN	Uncertain	-2.5	N
REVEL	Pathogenic	0.86
Sift	Uncertain	0.0060	D
Sift4G	Benign	0.080	T
Polyphen		0.99	D
Vest4		0.59
MutPred		0.82		Gain of sheet (P = 0.0827)
MVP		0.98
MPC		0.35
ClinPred		0.99	D
GERP RS		5.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.69
gMVP		0.59
Mutation Taster		=15/85	disease causing (ClinVar)

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	1.0
Splicevardb		3.0
SpliceAI score (max)		0.44		Details are displayed if max score is > 0.2
DS_DG_spliceai		0.29		Position offset: -4
DS_DL_spliceai		0.44		Position offset: 0

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

Other links and lift over

dbSNP: rs63751711; hg19: chr3-37053590; COSMIC: COSV51619014; COSMIC: COSV51619014;