The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_000249.4(MLH1):c.2042C>T (p.Ala681Val)

CA008313

90011 (ClinVar)

Gene: MLH1
Condition: Lynch syndrome 1
Inheritance Mode: Autosomal dominant inheritance
UUID: 0f212932-d140-4720-84c0-9bb167ebb160
Approved on: 2024-09-19
Published on: 2024-10-11

HGVS expressions

NM_000249.4:c.2042C>T
NM_000249.4(MLH1):c.2042C>T (p.Ala681Val)
NC_000003.12:g.37048956C>T
CM000665.2:g.37048956C>T
NC_000003.11:g.37090447C>T
CM000665.1:g.37090447C>T
NC_000003.10:g.37065451C>T
NG_007109.2:g.60607C>T
ENST00000413740.2:c.1668-1530C>T
ENST00000429117.6:c.1748C>T
ENST00000450420.6:c.1559-1530C>T
ENST00000456676.7:c.1896+1273C>T
ENST00000492474.6:c.1319C>T
ENST00000616768.6:c.1949C>T
ENST00000673673.2:c.1877C>T
ENST00000231790.8:c.2042C>T
ENST00000413212.2:c.*960C>T
ENST00000432299.6:c.*1874C>T
ENST00000447829.6:c.*1153C>T
ENST00000539477.6:c.1319C>T
ENST00000616768.5:c.986C>T
ENST00000673673.1:c.1830C>T
ENST00000673741.1:n.1076C>T
ENST00000673889.1:n.1424C>T
ENST00000673897.1:c.*1834C>T
ENST00000673899.1:c.1310C>T
ENST00000673947.1:c.*2182C>T
ENST00000673972.1:c.*1920C>T
ENST00000674019.1:c.1319C>T
ENST00000674111.1:c.*271C>T
ENST00000674125.1:n.753C>T
ENST00000231790.6:c.2042C>T
ENST00000413740.1:c.291-1530C>T
ENST00000435176.5:c.1748C>T
ENST00000450420.5:c.182-1530C>T
ENST00000455445.6:c.1319C>T
ENST00000456676.6:c.1871+1273C>T
ENST00000458205.6:c.1319C>T
ENST00000536378.5:c.1319C>T
ENST00000539477.5:c.1319C>T
NM_000249.3:c.2042C>T
NM_001167617.1:c.1748C>T
NM_001167618.1:c.1319C>T
NM_001167619.1:c.1319C>T
NM_001258271.1:c.1896+1273C>T
NM_001258273.1:c.1319C>T
NM_001258274.1:c.1319C>T
NM_001167617.2:c.1748C>T
NM_001167618.2:c.1319C>T
NM_001167619.2:c.1319C>T
NM_001258274.2:c.1319C>T
NM_001354615.1:c.1319C>T
NM_001354616.1:c.1319C>T
NM_001354617.1:c.1319C>T
NM_001354618.1:c.1319C>T
NM_001354619.1:c.1319C>T
NM_001354620.1:c.1748C>T
NM_001354621.1:c.1019C>T
NM_001354622.1:c.1019C>T
NM_001354623.1:c.1019C>T
NM_001354624.1:c.968C>T
NM_001354625.1:c.968C>T
NM_001354626.1:c.968C>T
NM_001354627.1:c.968C>T
NM_001354628.1:c.1949C>T
NM_001354629.1:c.1943C>T
NM_001354630.1:c.1877C>T
NM_001167617.3:c.1748C>T
NM_001167618.3:c.1319C>T
NM_001167619.3:c.1319C>T
NM_001258271.2:c.1896+1273C>T
NM_001258273.2:c.1319C>T
NM_001258274.3:c.1319C>T
NM_001354615.2:c.1319C>T
NM_001354616.2:c.1319C>T
NM_001354617.2:c.1319C>T
NM_001354618.2:c.1319C>T
NM_001354619.2:c.1319C>T
NM_001354620.2:c.1748C>T
NM_001354621.2:c.1019C>T
NM_001354622.2:c.1019C>T
NM_001354623.2:c.1019C>T
NM_001354624.2:c.968C>T
NM_001354625.2:c.968C>T
NM_001354626.2:c.968C>T
NM_001354627.2:c.968C>T
NM_001354628.2:c.1949C>T
NM_001354629.2:c.1943C>T
NM_001354630.2:c.1877C>T
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Uncertain Significance

Met criteria codes 2
PM2_Supporting PP4_Strong
Not Met criteria codes 1
PP3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for MLH1 Version 1.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
InSiGHT Hereditary Colorectal Cancer/Polyposis VCEP
The NM_000249.4: c.2042C>T variant in MLH1 is a missense variant predicted to cause substitution of Alanin by Valin at amino acid 681 (p.Ala681Val). This variant has been detected in at least three patient with colorectal or endometrial MSI-H / loss MLH1/PMS2 tumours (PP4_Strong). This variant is absent in gnomAD v2.1.1 using the non-cancer dataset and gnomAD v4.1 (PM2_Supporting). Due to insufficient evidence, this variant is classified as a variant of uncertain significance for Lynch-Syndrome based on the ACMG/AMP criteria applied, as specified by the ClinGen InSiGHT Hereditary Colorectal Cancer/ Polyposis VCEP: PP4_STR, PM2_SUP (VCEP specifications version 1).
Met criteria codes
PM2_Supporting
Absent in gnomAD v2.1.1 using the non-cancer dataset and gnomAD v4.1
PP4_Strong
At least three patient with colorectal or endometrial MSI-H tumours (PP4).
Not Met criteria codes
PP3
Missense variant with MAPP/PP2 score=0.20.
Curation History
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