ARL3 p.Thr85=
c.255C>T · rs201451573 · VCV1136495
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0497%, 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 -1.3 | GERP -4.8 |
| Overall | ||
| CADD | 5.626 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0497%
Middle Eastern · 3/6,032 alleles
Filtering AF
0.0135%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00722%
Overall
0.00101%
16/1,584,076 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0497% | 2,011 |
| Remaining individualsnot grpmax-eligible | 0.00976% | 10,243 |
| South Asian | 0.00221% | 45,189 |
| European (non-Finnish) | 0.000433% | 230,687 |
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.Thr85=
- Coding
- c.255C>T
- MANE Select
- NM_004311
- dbSNP
- rs201451573
- Type
- single nucleotide variant
- Location
- chr10:102699382 (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-thr85 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown