ARMC2 p.Leu135=
c.405A>G · rs144751024 · VCV2656823
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0394%, nfe)
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 -3.4 | GERP -5.1 |
| Overall | ||
| CADD | 1.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0394%
European (non-Finnish) · 465/1,179,860 alleles
Filtering AF
0.0364%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0352%
Overall
0.0308%
497/1,613,840 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0394% | 2,537 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,470 |
| Admixed American | 0.02% | 5,000 |
| Middle Eastern | 0.0164% | 6,084 |
| African / African-American | 0.00133% | 74,924 |
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.Leu135=
- Coding
- c.405A>G
- MANE Select
- NM_032131
- dbSNP
- rs144751024
- Type
- single nucleotide variant
- Location
- chr6:108868937 (GRCh38)
- Gene constraint
- LOEUF 0.936 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.57
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-leu135 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown