Is FERMT3 p.Pro27Ser (c.79C>T) pathogenic?

FERMT3 p.Pro27Ser (c.79C>T) is classified Uncertain significance in FERMT3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-12-15). AlphaMissense: likely benign (0.0782); Absent from gnomAD v4.1; Associated with Inborn genetic diseases.

What condition is associated with FERMT3 p.Pro27Ser (c.79C>T)?

FERMT3 p.Pro27Ser (c.79C>T) is associated with Inborn genetic diseases (ClinVar).

How common is FERMT3 p.Pro27Ser (c.79C>T) in the general population?

FERMT3 p.Pro27Ser (c.79C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about FERMT3 p.Pro27Ser (c.79C>T)?

AlphaMissense predicts likely benign (score 0.0782) — an in-silico prediction, not a clinical call.

FERMT3 p.Pro27Ser

c.79C>T · VCV4836996

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0782 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.0782	likely benign
REVEL	0.133	moderately benign-leaning
SaProt	LLR -6.86	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.9	GERP -0.63, phastCons 0.84
Regional constraint	o/e 0.83	unconstrained · MANE · 16 kb · p 2.9e-07 · regional, not allelic
Overall
CADD	15.42	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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: FERMT3
Protein: p.Pro27Ser
Coding: c.79C>T
MANE Select: NM_031471
Type: single nucleotide variant
Location: chr11:64207443 (GRCh38)
Gene constraint: LOEUF 0.556 · pLI 0.17 (gnomAD)
Structure: AlphaFold pLDDT 83.80 · 6 PDB
Residue 27: a turn

Full FERMT3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

FERMT3 p.Ala570Thr Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg200Gln Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg212His Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg234Trp Uncertain significance ★★ same condition
FERMT3 p.Arg538Cys Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg573Gln Uncertain significance ★★ ⚠ same condition
FERMT3 p.Arg603Gln Uncertain significance ★★ ⚠ same condition
FERMT3 p.Asp206Asn Uncertain significance ★★ ⚠ 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/fermt3-p-pro27ser (accessed [today's date]).

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