Is MSH6 p.Arg583= (c.1749G>A) pathogenic?

MSH6 p.Arg583= (c.1749G>A) is classified Likely benign in MSH6 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-07-06). Absent from gnomAD v4.1; Associated with Hereditary nonpolyposis colorectal neoplasms.

What condition is associated with MSH6 p.Arg583= (c.1749G>A)?

MSH6 p.Arg583= (c.1749G>A) is associated with Hereditary nonpolyposis colorectal neoplasms (ClinVar).

How common is MSH6 p.Arg583= (c.1749G>A) in the general population?

MSH6 p.Arg583= (c.1749G>A) is absent from gnomAD v4.1 (gnomAD).

MSH6 p.Arg583=

c.1749G>A · rs2104365231 · VCV2736397

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Hereditary nonpolyposis colorectal neoplasms

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.5	GERP 1.3, phastCons 1
Overall
CADD	8.715	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: MSH6
Protein: p.Arg583=
Coding: c.1749G>A
MANE Select: NM_000179
dbSNP: rs2104365231
Type: single nucleotide variant
Location: chr2:47799732 (GRCh38)
Gene constraint: LOEUF 0.841 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 77.93 · 8 PDB
Residue 583: an α-helix

Full MSH6 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Hereditary nonpolyposis colorectal neoplasms — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MSH6 p.Arg583Thr Conflicting classifications of pathogenicity ★ ⚠ same residue
MSH6 p.Arg583Ter Pathogenic ★ same residue
MSH6 p.Arg583Gly Uncertain significance ★★ ⚠ same residue
MSH6 p.Arg583Lys Uncertain significance ★ ⚠ same residue
MSH6 p.Arg583Met Uncertain significance ★ ⚠ same residue
MSH6 c.3173-3C>G Pathogenic/Likely pathogenic ★★ same condition
MSH6 c.3557-1G>A Likely pathogenic ★★ same condition
MSH6 c.3557-1G>C Pathogenic/Likely pathogenic ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/msh6-p-arg583 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown