Is ABHD10 p.Ser17Arg (c.51C>A) pathogenic?

ABHD10 p.Ser17Arg (c.51C>A) is classified Likely benign in ABHD10 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-09-17). AlphaMissense: likely benign (0.1041); Absent from gnomAD v4.1.

How common is ABHD10 p.Ser17Arg (c.51C>A) in the general population?

ABHD10 p.Ser17Arg (c.51C>A) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ABHD10 p.Ser17Arg (c.51C>A)?

AlphaMissense predicts likely benign (score 0.1041) — an in-silico prediction, not a clinical call.

ABHD10 p.Ser17Arg

c.51C>A · rs2473208459 · VCV2251042

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1041 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.1041	likely benign
REVEL	0.07	moderately benign-leaning
SaProt	LLR -6.01	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 0.34	GERP -0.87, phastCons 0.34
Regional constraint	o/e 0.93	unconstrained · MANE · 13 kb · p 0.15 · regional, not allelic
Overall
CADD	11.98	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

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: ABHD10
Protein: p.Ser17Arg
Coding: c.51C>A
MANE Select: NM_018394
dbSNP: rs2473208459
Type: single nucleotide variant
Location: chr3:111979112 (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-ser17arg (accessed [today's date]).

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