Is ABHD13 p.Ile89Val (c.265A>G) pathogenic?

ABHD13 p.Ile89Val (c.265A>G) is classified Uncertain significance in ABHD13 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-10-01). AlphaMissense: likely benign (0.0724); Very rare (popmax 0.000678%, nfe).

How common is ABHD13 p.Ile89Val (c.265A>G) in the general population?

ABHD13 p.Ile89Val (c.265A>G) is very rare (popmax 0.000678%, nfe) (gnomAD).

What do computational predictors say about ABHD13 p.Ile89Val (c.265A>G)?

AlphaMissense predicts likely benign (score 0.0724) — an in-silico prediction, not a clinical call.

ABHD13 p.Ile89Val

c.265A>G · VCV3423739

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0724 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.000678%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0724	likely benign
REVEL	0.098	moderately benign-leaning
SaProt	LLR -5.84	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 4.7	phastCons 1
Regional constraint	o/e 0.75	unconstrained · MANE · 1,010 bp · p 5.2e-07 · regional, not allelic
Overall
CADD	12.05	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 0.000678% European (non-Finnish) · 8/1,179,610 alleles

Filtering AF 0.000292% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000211%

Overall 0.000496% 8/1,613,408 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: ABHD13
Protein: p.Ile89Val
Coding: c.265A>G
MANE Select: NM_032859
Type: single nucleotide variant
Location: chr13:108229483 (GRCh38)
Gene constraint: LOEUF 0.504 · pLI 0.98 (gnomAD)
Structure: AlphaFold pLDDT 92.06

Full ABHD13 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABHD13 p.Arg130Gly Uncertain significance ★ ⚠ same type
ABHD13 p.Arg192Cys Uncertain significance ★ ⚠ same type
ABHD13 p.Arg236His Uncertain significance ★ ⚠ same type
ABHD13 p.Arg98His Uncertain significance ★ ⚠ same type
ABHD13 p.Asn299Ser Uncertain significance ★ ⚠ same type
ABHD13 p.Asn333Asp Uncertain significance ★ ⚠ same type
ABHD13 p.Gln313Leu Uncertain significance ★ ⚠ same type
ABHD13 p.Gly108Glu 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/abhd13-p-ile89val (accessed [today's date]).

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