Is FABP5 p.Phe89Val (c.265T>G) pathogenic?

FABP5 p.Phe89Val (c.265T>G) is classified Uncertain significance in FABP5 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-08-19). AlphaMissense: likely benign (0.2721); Very rare (popmax 0.00017%, nfe).

How common is FABP5 p.Phe89Val (c.265T>G) in the general population?

FABP5 p.Phe89Val (c.265T>G) is very rare (popmax 0.00017%, nfe) (gnomAD).

What do computational predictors say about FABP5 p.Phe89Val (c.265T>G)?

AlphaMissense predicts likely benign (score 0.2721) — an in-silico prediction, not a clinical call.

FABP5 p.Phe89Val

c.265T>G · VCV3511391

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2721 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00017%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.2721	likely benign
REVEL	0.055	moderately benign-leaning
SaProt	LLR -5.88	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 1.1	GERP -0.64, phastCons 0.93
Regional constraint	o/e 0.75	unconstrained · MANE · 3,968 bp · p 0.0014 · regional, not allelic
Overall
CADD	20.9	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

Grpmax group 0.00017% European (non-Finnish) · 2/1,178,888 alleles

Filtering AF 2.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.1e-05%

Overall 0.00131% 2/152,168 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: FABP5
Protein: p.Phe89Val
Coding: c.265T>G
Type: single nucleotide variant
Location: chr8:81283885 (GRCh38)

Full FABP5 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

FABP5 p.Arg12His Uncertain significance ★ ⚠ same type
FABP5 p.Arg33Gln Uncertain significance ★ ⚠ same type
FABP5 p.Gln5His Uncertain significance ★ ⚠ same type
FABP5 p.Gln5Lys Uncertain significance ★ ⚠ same type
FABP5 p.Glu132Val Uncertain significance ★ same type
FABP5 p.Glu8Lys Uncertain significance ★ ⚠ same type
FABP5 p.Gly29Glu Uncertain significance ★ ⚠ same type
FABP5 p.Gly9Arg Uncertain significance ★ ⚠ same type

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/fabp5-p-phe89val (accessed [today's date]).

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