Is ARMC2 p.Ala184Val (c.551C>T) pathogenic?

ARMC2 p.Ala184Val (c.551C>T) is classified Benign in ARMC2 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2024-06-05). AlphaMissense: likely benign (0.0918); Rare (popmax 0.748%, eas); Associated with ARMC2-related disorder.

What condition is associated with ARMC2 p.Ala184Val (c.551C>T)?

ARMC2 p.Ala184Val (c.551C>T) is associated with ARMC2-related disorder (ClinVar).

How common is ARMC2 p.Ala184Val (c.551C>T) in the general population?

ARMC2 p.Ala184Val (c.551C>T) is rare (popmax 0.748%, eas) (gnomAD).

What do computational predictors say about ARMC2 p.Ala184Val (c.551C>T)?

AlphaMissense predicts likely benign (score 0.0918) — an in-silico prediction, not a clinical call.

ARMC2 p.Ala184Val

c.551C>T · rs181478757 · VCV3040116

Benign No assertion criteria

Classification

Benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0918 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.748%, eas)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

ARMC2-related disorder

Computational evidence

Protein change
AlphaMissense	0.0918	likely benign
REVEL	0.16	moderately benign-leaning
SaProt	LLR -6.08	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 2.2	GERP 1.7, phastCons 0.038
Regional constraint	o/e 0.89	unconstrained · MANE · 119 kb · p 0.00055 · regional, not allelic
Overall
CADD	15.65	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 0.748% East Asian · 335/44,776 alleles

Filtering AF 0.682% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.656%

Overall 0.0283% 456/1,612,734 alleles · rare

Ancestry group	Frequency	1 in
East Asiangrpmax	0.748%	134
Remaining individualsnot grpmax-eligible	0.136%	735
African / African-American	0.02%	4,999
Admixed American	0.0167%	5,987
South Asian	0.00661%	15,121
European (non-Finnish)	0.000424%	235,873

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.Ala184Val
Coding: c.551C>T
MANE Select: NM_032131
dbSNP: rs181478757
Type: single nucleotide variant
Location: chr6:108876230 (GRCh38)
Gene constraint: LOEUF 0.936 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.57
Residue 184: a UniProt-annotated variant site (in spgf38; uncertain significance)

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

Disease context

ARMC2-related disorder

Similar variants

ARMC2 p.Ile185Val Conflicting classifications of pathogenicity ⚠ same condition
ARMC2 c.219-4C>T Benign same condition
ARMC2 p.Ala593= Benign same condition
ARMC2 p.Gly438= Benign same condition
ARMC2 p.Ile630Val Benign same condition
ARMC2 p.Met166Thr Benign same condition
ARMC2 p.Pro622= Likely benign same condition
ARMC2 p.Pro99= Benign same condition

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-ala184val (accessed [today's date]).

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