ARMC9 p.Pro800=
c.2400C>G · rs775538265 · VCV1092159
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.251%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -7.7 | GERP -3 |
| Overall | ||
| CADD | 0.256 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.251%
Middle Eastern · 15/5,984 alleles
Filtering AF
0.154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.125%
Overall
0.00248%
38/1,534,390 alleles · rare
exomes 37/1,382,062 · genomes 1/152,328 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.251% | 399 |
| South Asian | 0.0119% | 8,385 |
| Remaining individualsnot grpmax-eligible | 0.0117% | 8,562 |
| European (non-Finnish) | 0.000524% | 190,971 |
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
- ARMC9
- Protein
- p.Pro800=
- Coding
- c.2400C>G
- MANE Select
- NM_001352754
- dbSNP
- rs775538265
- Type
- single nucleotide variant
- Location
- chr2:231370091 (GRCh38)
- Gene constraint
- LOEUF 0.975 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 71.71
- Residue 800
- the 'disordered' region
Similar variants
- ARMC9 c.1773+1G>A Likely pathogenic ★★ same type
- ARMC9 c.178-1G>A Likely pathogenic ★★ same type
- ARMC9 c.178-2A>C Likely pathogenic ★★ same type
- ARMC9 p.Arg299Ter Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Arg343Cys Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Arg87Ter Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Thr293= Pathogenic/Likely pathogenic ★★ same type
- ARMC9 p.Ala397Val 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/armc9-p-pro800 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown