Is ABHD10 p.Pro27Ser (c.79C>T) pathogenic?

ABHD10 p.Pro27Ser (c.79C>T) is classified Uncertain significance in ABHD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-08-02). AlphaMissense: likely benign (0.0811); Rare (popmax 0.14%, nfe).

How common is ABHD10 p.Pro27Ser (c.79C>T) in the general population?

ABHD10 p.Pro27Ser (c.79C>T) is rare (popmax 0.14%, nfe) (gnomAD).

What do computational predictors say about ABHD10 p.Pro27Ser (c.79C>T)?

AlphaMissense predicts likely benign (score 0.0811) — an in-silico prediction, not a clinical call.

ABHD10 p.Pro27Ser

c.79C>T · rs147373641 · VCV2341833

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0811 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.14%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0811	likely benign
REVEL	0.031	moderately benign-leaning
SaProt	LLR -5.95	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 0.088	GERP -1.3
Regional constraint	o/e 0.93	unconstrained · MANE · 13 kb · p 0.15 · regional, not allelic
Overall
CADD	5.784	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 0.14% European (non-Finnish) · 1,655/1,179,766 alleles

Filtering AF 0.135% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.132%

Overall 0.117% 1,883/1,613,230 alleles · rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.14%	713
Remaining individualsnot grpmax-eligible	0.134%	744
Admixed American	0.11%	909
Middle Eastern	0.0826%	1,211
South Asian	0.034%	2,937
African / African-American	0.0333%	3,003
Ashkenazi Jewishnot grpmax-eligible	0.0237%	4,225
Finnishnot grpmax-eligible	0.0158%	6,345

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: ABHD10
Protein: p.Pro27Ser
Coding: c.79C>T
MANE Select: NM_018394
dbSNP: rs147373641
Type: single nucleotide variant
Location: chr3:111979140 (GRCh38)
Gene constraint: LOEUF 1.037 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 86.70

Full ABHD10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABHD10 p.Ala106Gly Uncertain significance ★ ⚠ same type
ABHD10 p.Ala10Val Uncertain significance ★ ⚠ same type
ABHD10 p.Ala11Asp Uncertain significance ★ ⚠ same type
ABHD10 p.Ala48Val Uncertain significance ★ ⚠ same type
ABHD10 p.Arg165Leu Uncertain significance ★ ⚠ same type
ABHD10 p.Arg37Trp Uncertain significance ★ ⚠ same type
ABHD10 p.Arg44Gln Uncertain significance ★ ⚠ same type
ABHD10 p.Asn187Asp 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/abhd10-p-pro27ser (accessed [today's date]).

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