rs63750710

Positions:

• chr3-37020411-A-C
• chr3-37020411-A-G
• chr3-37020411-A-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM2 PM5 PP3_Strong PP5_Very_Strong

The NM_000249.4(MLH1):​c.986A>C​(p.His329Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. H329N) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 32)
• Consequence: MLH1 NM_000249.4 missense
• Clinical Significance: Pathogenic reviewed by expert panel P:3 U:1
• Conservation: PhyloP100: 8.88

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 (HGNC:):

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chr3-37020410-C-A is described in Lovd as [Pathogenic].
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.969
• PP5: Variant 3-37020411-A-C is Pathogenic according to our data. Variant chr3-37020411-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 17085.Status of the report is reviewed_by_expert_panel, 3 stars. Variant chr3-37020411-A-C is described in Lovd as [Pathogenic]. Variant chr3-37020411-A-C is described in Lovd as [Benign]. Variant chr3-37020411-A-C is described in Lovd as [Likely_pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MLH1	NM_000249.4	c.986A>C	p.His329Pro	missense_variant	11/19	ENST00000231790.8	NP_000240.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
MLH1	ENST00000231790.8	c.986A>C	p.His329Pro	missense_variant	11/19	1	NM_000249.4	ENSP00000231790.3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:3 Uncertain:1

Revision: reviewed by expert panel

Submissions by phenotype

Colorectal cancer, hereditary nonpolyposis, type 2 Pathogenic:1 Uncertain:1

Uncertain significance, criteria provided, single submitter	clinical testing	Baylor Genetics	Apr 07, 2023	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Sep 01, 1997	- -

Lynch syndrome Pathogenic:1

Pathogenic, reviewed by expert panel

research

International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

Sep 05, 2013

Variant causes splicing aberrations (full inactivation of variant allele) -

Hereditary cancer-predisposing syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Jul 30, 2021

The p.H329P pathogenic mutation (also known as c.986A>C), located in coding exon 11 of the MLH1 gene, results from an A to C substitution at nucleotide position 986. The histidine at codon 329 is replaced by proline, an amino acid with similar properties. This alteration is identified in multiple individuals diagnosed with Lynch-related tumors that demonstrated high microsatellite instability and loss of MLH1 on immunohistochemistry (IHC) and/or whose family history met Amsterdam Criteria (Müller-Koch Y et al. Eur. J. Med. Res. 2001 Nov;6:473-82; Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Kansikas M et al. Hum Mutat. 2011 Jan;32:107-1; Hardt K et al. Fam Cancer. 2011 Jun;10:273-84; Ambry internal data). In an individual diagnosed with colorectal and endometrial cancer at less than 50 years of age with loss of MLH1 and PMS2 on IHC, cDNA long-range RT-PCR analysis of full-length MLH1 transcripts demonstrated that this alteration results in abnormal splicing (Morak M et al. Eur J Hum Genet. 2019 12;27:1808-1820). In addition, an unpublished observation reported that the presence of this alteration completely abrogates normal splicing of the mutant allele in cDNA-analysis (Hardt K et al. Fam Cancer. 2011 Jun;10:273-84). In two functional studies, compared to wild-type MLH1, p.H329P demonstrated similar MMR efficiency and decreased expression in one study but reduced MMR activity and retained expression in the other study (Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49; Takahashi M et al. Cancer Res. 2007 May;67:4595-604). In addition, this alteration demonstrated aberrant nuclear localization in 293T human cells (Raevaara TE et al. Gastroenterology. 2005 Aug;129:537-49). This variant is considered to be rare based on population cohorts in the Genome Aggregation Database (gnomAD). This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Based on the supporting evidence, this alteration is interpreted as a disease-causing mutation. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	0.87
BayesDel_addAF	Pathogenic	0.39	D
BayesDel_noAF	Pathogenic	0.33
CADD	Uncertain	24
DANN	Uncertain	0.98
DEOGEN2	Uncertain	0.78	D;.;.;.;.;.;.
Eigen	Uncertain	0.57
Eigen_PC	Uncertain	0.63
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Uncertain	0.94	D;D;.;.;.;D;D
M_CAP	Uncertain	0.10	D
MetaRNN	Pathogenic	0.97	D;D;D;D;D;D;D
MetaSVM	Uncertain	-0.18	T
MutationAssessor	Uncertain	2.3	M;.;.;.;.;.;.
PrimateAI	Uncertain	0.68	T
PROVEAN	Uncertain	-3.6	D;D;D;D;D;D;D
REVEL	Pathogenic	0.82
Sift	Benign	0.24	T;T;T;T;T;T;T
Sift4G	Benign	0.26	T;T;T;T;T;T;T
Polyphen		0.93	P;.;.;.;.;.;.
Vest4		0.96
MutPred		0.90		Gain of disorder (P = 0.0865);.;.;.;.;.;.;
MVP		0.96
MPC		0.37
ClinPred		0.93	D
GERP RS		5.8
Varity_R		0.93
gMVP		0.77

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

Other links and lift over

dbSNP: rs63750710; hg19: chr3-37061902;