Is PMS2 p.Arg282del (c.846_848del) pathogenic?

PMS2 p.Arg282del (c.846848del) is classified Uncertain significance in PMS2 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2021-08-27). Very rare (popmax 0.00133%, afr); Associated with Hereditary nonpolyposis colorectal neoplasms.

What condition is associated with PMS2 p.Arg282del (c.846_848del)?

PMS2 p.Arg282del (c.846_848del) is associated with Hereditary nonpolyposis colorectal neoplasms, hereditary neoplastic syndrome (ClinVar).

How common is PMS2 p.Arg282del (c.846_848del) in the general population?

PMS2 p.Arg282del (c.846_848del) is very rare (popmax 0.00133%, afr) (gnomAD).

PMS2 p.Arg282del

c.846_848del · rs776688670 · VCV525663

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00133%, afr)

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 · substitutions only
Constraint at this position
Conservation	phyloP 0.23	phastCons 0.46

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00133% African / African-American · 1/74,960 alleles

Overall 6.84e-05% 1/1,461,672 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: PMS2
Protein: p.Arg282del
Coding: c.846_848del
MANE Select: NM_000535
dbSNP: rs776688670
Type: Deletion
Location: chr7:5995589 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB
Residue 282: a β-strand

Full PMS2 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

Also linked: hereditary neoplastic syndrome

Similar variants

PMS2 p.Arg282Gly Uncertain significance ★★ ⚠ same residue
PMS2 p.Arg282= Benign/Likely benign ★★ same residue
PMS2 p.Arg282Lys Uncertain significance ★ ⚠ same residue
PMS2 p.Arg282Ser Uncertain significance ★ ⚠ same residue
PMS2 c.989-296_1144+706del Pathogenic ★★★ same condition
PMS2 p.Glu180_Tyr181insTer Pathogenic ★★★ same condition
PMS2 p.Leu731fs Pathogenic ★★★ same condition
PMS2 p.Phe788fs 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/pms2-p-arg282del (accessed [today's date]).

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