PMS2 p.Val698=
c.2094G>A · VCV3622777
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00111%, sas)
Conditions
1
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 1.9 | phastCons 1 |
| Overall | ||
| CADD | 15.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00111%
South Asian · 1/90,048 alleles
Overall
6.25e-05%
1/1,599,044 alleles · very rare
exomes 1/1,447,334 · genomes 0/151,710 · joint denominator
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.Val698=
- Coding
- c.2094G>A
- MANE Select
- NM_000535
- Type
- single nucleotide variant
- Location
- chr7:5982904 (GRCh38)
- Gene constraint
- LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 71.37 · 9 PDB
Similar variants
- PMS2 p.Val698Ala Uncertain significance ★★ ⚠ same residue
- PMS2 p.Val698Glu Uncertain significance ★★ ⚠ same residue
- PMS2 p.Val698Gly Uncertain significance ★★ ⚠ same residue
- PMS2 p.Val698Leu Uncertain significance ★★ ⚠ same residue
- PMS2 p.Val698Met Uncertain significance ★★ ⚠ same residue
- PMS2 c.1145-2A>G Likely pathogenic ★★ same condition
- PMS2 c.164-1G>A Pathogenic/Likely pathogenic ★★ same condition
- PMS2 c.164-1G>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/pms2-p-val698 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown