ARL3 p.Ile92=
c.276C>T · rs138670218 · VCV1108229
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0169%, 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 0.69 | GERP -4.5, phastCons 0.97 |
| Overall | ||
| CADD | 10.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0169%
Middle Eastern · 1/5,920 alleles
Filtering AF
0.00455%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00415%
Overall
0.00508%
81/1,595,168 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0169% | 5,920 |
| Finnishnot grpmax-eligible | 0.011% | 9,067 |
| European (non-Finnish) | 0.00565% | 17,712 |
| Remaining individualsnot grpmax-eligible | 0.00487% | 20,548 |
| South Asian | 0.00451% | 22,198 |
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
- ARL3
- Protein
- p.Ile92=
- Coding
- c.276C>T
- MANE Select
- NM_004311
- dbSNP
- rs138670218
- Type
- single nucleotide variant
- Location
- chr10:102689932 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI 0.93 (gnomAD)
- Structure
- AlphaFold pLDDT 92.73
Similar variants
- ARL3 p.Gly70Glu Pathogenic/Likely pathogenic ★★ same type
- ARL3 c.3+1G>A Uncertain significance ★★ same type
- ARL3 c.3+2T>C Uncertain significance ★★ same type
- ARL3 c.3+3G>T Uncertain significance ★★ same type
- ARL3 c.316-2A>G Uncertain significance ★★ same type
- ARL3 p.Ala13Ser Uncertain significance ★★ ⚠ same type
- ARL3 p.Ala140Val Uncertain significance ★★ same type
- ARL3 p.Ala179Pro 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/arl3-p-ile92 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown