Is ARMC10 p.Ser263Pro (c.787T>C) pathogenic?

ARMC10 p.Ser263Pro (c.787T>C) is classified Uncertain significance in ARMC10 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-09-11). AlphaMissense: likely benign (0.1777); Absent from gnomAD v4.1.

How common is ARMC10 p.Ser263Pro (c.787T>C) in the general population?

ARMC10 p.Ser263Pro (c.787T>C) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ARMC10 p.Ser263Pro (c.787T>C)?

AlphaMissense predicts likely benign (score 0.1777) — an in-silico prediction, not a clinical call.

ARMC10 p.Ser263Pro

c.787T>C · VCV3430631

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.1777 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.1777	likely benign
REVEL	0.298	indeterminate
SaProt	LLR -12.63	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.4	GERP -3.1, phastCons 1
Regional constraint	o/e 0.27	constrained · MANE · 245 bp · p 1.7e-12 · regional, not allelic
Overall
CADD	21.9	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: ARMC10
Protein: p.Ser263Pro
Coding: c.787T>C
MANE Select: NM_031905
Type: single nucleotide variant
Location: chr7:103098308 (GRCh38)
Gene constraint: LOEUF 1.341 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 80.88

Full ARMC10 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARMC10 p.Ala126Pro Uncertain significance ★ ⚠ same type
ARMC10 p.Ala132Ser Uncertain significance ★ ⚠ same type
ARMC10 p.Ala198Thr Uncertain significance ★ ⚠ same type
ARMC10 p.Ala298Gly Uncertain significance ★ ⚠ same type
ARMC10 p.Ala330Gly Uncertain significance ★ ⚠ same type
ARMC10 p.Ala7Gly Uncertain significance ★ ⚠ same type
ARMC10 p.Arg279Gln Uncertain significance ★ ⚠ same type
ARMC10 p.Arg33Trp 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/armc10-p-ser263pro (accessed [today's date]).

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