Is ABHD18 p.Val55Ala (c.164T>C) pathogenic?

ABHD18 p.Val55Ala (c.164T>C) is classified Uncertain significance in ABHD18 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-07). AlphaMissense: likely pathogenic (0.8857); Absent from gnomAD v4.1.

How common is ABHD18 p.Val55Ala (c.164T>C) in the general population?

ABHD18 p.Val55Ala (c.164T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABHD18 p.Val55Ala (c.164T>C)?

AlphaMissense predicts likely pathogenic (score 0.8857) — an in-silico prediction, not a clinical call.

ABHD18 p.Val55Ala

c.164T>C · VCV3786786

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.8857 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,536,502)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.8857	likely pathogenic
REVEL	0.258	benign-leaning
SaProt	LLR -11.23	damaging
⇒ AlphaMissense and SaProt call this damaging; REVEL does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.7	GERP 1.9, phastCons 1
Regional constraint	o/e 0.99	unconstrained · MANE · 38 kb · p 0.8 · regional, not allelic
Overall
CADD	25.2	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,536,502). 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: ABHD18
Protein: p.Val55Ala
Coding: c.164T>C
MANE Select: NM_001358451
Type: single nucleotide variant
Location: chr4:127984410 (GRCh38)
Gene constraint: LOEUF 1.028 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.82

Full ABHD18 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

MFSD8 c.-100G>C Benign ★★ same type
MFSD8 c.-75-215A>G Benign ★★ same type
MFSD8 c.-75-333C>G Benign ★★ same type
ABHD18 p.Ala136Asp Uncertain significance ★ ⚠ same type
ABHD18 p.Ala439Thr Uncertain significance ★ ⚠ same type
ABHD18 p.Ala78Thr Uncertain significance ★ ⚠ same type
ABHD18 p.Arg11Gln Uncertain significance ★ ⚠ same type
ABHD18 p.Arg11Trp 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/abhd18-p-val55ala (accessed [today's date]).

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