Is ARMC2 p.Pro275Leu (c.824C>T) pathogenic?

ARMC2 p.Pro275Leu (c.824C>T) is classified Uncertain significance in ARMC2 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-01-29). AlphaMissense: likely benign (0.2769); Ultra-rare (popmax 0.0924%, afr).

How common is ARMC2 p.Pro275Leu (c.824C>T) in the general population?

ARMC2 p.Pro275Leu (c.824C>T) is ultra-rare (popmax 0.0924%, afr) (gnomAD).

What do computational predictors say about ARMC2 p.Pro275Leu (c.824C>T)?

AlphaMissense predicts likely benign (score 0.2769) — an in-silico prediction, not a clinical call.

ARMC2 p.Pro275Leu

c.824C>T · rs186501123 · VCV2408803

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2769 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0924%, afr)

Missense predictors

1/2 damaging

AlphaMissense, SaProt · REVEL no call

Computational evidence

Protein change
AlphaMissense	0.2769	likely benign
REVEL	0.34	indeterminate
SaProt	LLR -12.60	damaging
⇒ SaProt calls this damaging; AlphaMissense does not; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.8, phastCons 1
Regional constraint	o/e 0.89	unconstrained · MANE · 119 kb · p 0.00055 · regional, not allelic
Overall
CADD	25.0	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

Grpmax group 0.0924% African / African-American · 69/74,714 alleles

Filtering AF 0.0748% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0685%

Overall 0.0102% 165/1,612,308 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0924%	1,083
Remaining individualsnot grpmax-eligible	0.0112%	8,916
European (non-Finnish)	0.00729%	13,714
Admixed American	0.00501%	19,944

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: ARMC2
Protein: p.Pro275Leu
Coding: c.824C>T
MANE Select: NM_032131
dbSNP: rs186501123
Type: single nucleotide variant
Location: chr6:108899769 (GRCh38)
Gene constraint: LOEUF 0.936 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.57
Residue 275: a UniProt-annotated variant site (in spgf38; uncertain significance)

Full ARMC2 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ARMC2 c.2153-1G>C Likely pathogenic ★ same type
ARMC2 p.Asn743Asp Likely pathogenic ★ same type
ARMC2 p.Ala123Val Uncertain significance ★ ⚠ same type
ARMC2 p.Ala143Thr Uncertain significance ★ ⚠ same type
ARMC2 p.Ala231Thr Uncertain significance ★ ⚠ same type
ARMC2 p.Ala260Pro Uncertain significance ★ ⚠ same type
ARMC2 p.Ala292Asp Uncertain significance ★ ⚠ same type
ARMC2 p.Ala495Val 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/armc2-p-pro275leu (accessed [today's date]).

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