Is PMS2 p.Arg107= (c.321G>A) pathogenic?

PMS2 p.Arg107= (c.321G>A) is classified Benign/Likely benign in PMS2 (ClinVar, Multiple submitters, 10 submitters; last evaluated 2025-11-11). Very rare (popmax 0.00167%, amr); Associated with hereditary neoplastic syndrome.

What condition is associated with PMS2 p.Arg107= (c.321G>A)?

PMS2 p.Arg107= (c.321G>A) is associated with hereditary neoplastic syndrome, Lynch syndrome, breast cancer (ClinVar).

How common is PMS2 p.Arg107= (c.321G>A) in the general population?

PMS2 p.Arg107= (c.321G>A) is very rare (popmax 0.00167%, amr) (gnomAD).

PMS2 p.Arg107=

c.321G>A · rs756420858 · VCV231811

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 10 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00167%, amr)

Conditions

hereditary neoplastic syndrome

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 -0.12	phastCons 0.56
Overall
CADD	7.727	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00167% Admixed American · 1/59,956 alleles

Filtering AF 0.000429% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000313%

Overall 0.000688% 11/1,598,118 alleles · very rare

Ancestry group	Frequency	1 in
Admixed Americangrpmax	0.00167%	59,956
European (non-Finnish)	0.000849%	117,820

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.Arg107=
Coding: c.321G>A
MANE Select: NM_000535
dbSNP: rs756420858
Type: single nucleotide variant
Location: chr7:6003722 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB
Residue 107: a UniProt-annotated variant site (in mmrcs4; decreased dna mismatch repair activity); a β-strand

Full PMS2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hereditary neoplastic syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Lynch syndrome breast cancer Lynch syndrome 4

Similar variants

PMS2 p.Arg107Trp Pathogenic/Likely pathogenic ★★ same residue
PMS2 p.Arg107Gln Uncertain significance ★★ ⚠ same residue
PMS2 p.Arg107Leu Uncertain significance ★★ ⚠ same residue
PMS2 p.Arg107Pro Uncertain significance ★★ ⚠ same residue
PMS2 p.Arg107fs Pathogenic ★ same residue
PMS2 c.1144+2T>A Likely pathogenic ★★★ same condition
PMS2 c.163+2T>C Likely pathogenic ★★★ same condition
PMS2 c.164-2A>G 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/pms2-p-arg107 (accessed [today's date]).

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