Is PMS2 p.Phe267fs (c.801_802del) pathogenic?

PMS2 p.Phe267fs (c.801802del) is classified Pathogenic in PMS2 (ClinVar, Single submitter, 1 submitter; last evaluated 2018-02-11). No allele count reported in gnomAD v4.1 (AN 1,459,458); Associated with hereditary neoplastic syndrome.

What condition is associated with PMS2 p.Phe267fs (c.801_802del)?

PMS2 p.Phe267fs (c.801_802del) is associated with hereditary neoplastic syndrome (ClinVar).

How common is PMS2 p.Phe267fs (c.801_802del) in the general population?

PMS2 p.Phe267fs (c.801_802del) is no allele count reported in gnomAD v4.1 (AN 1,459,458) (gnomAD).

PMS2 p.Phe267fs

c.801_802del · rs267608149 · VCV1761644

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,459,458)

Conditions

hereditary neoplastic syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 7 of 15
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.065	phastCons 0.003

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,459,458). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PMS2
Protein: p.Phe267fs
Coding: c.801_802del
MANE Select: NM_000535
dbSNP: rs267608149
Type: Deletion
Location: chr7:5997327 (GRCh38)
Gene constraint: LOEUF 0.898 · pLI <0.01 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 71.37 · 9 PDB

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

Similar variants

PMS2 p.Phe267Cys Uncertain significance ★★ ⚠ same residue
PMS2 p.Phe267= Benign/Likely benign ★★ same residue
PMS2 p.Phe267Ter Pathogenic ★ same residue
PMS2 p.Phe267Leu 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-phe267fs (accessed [today's date]).

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