ARL3 p.Ala38=
c.114A>G · rs139645455 · VCV1165297
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.52%, sas)
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 -4.8 |
| Overall | ||
| CADD | 7.564 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.52%
South Asian · 1,377/90,876 alleles
Filtering AF
1.45%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.42%
Overall
0.117%
1,877/1,611,100 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.52% | 66 |
| Middle Eastern | 0.341% | 293 |
| Remaining individualsnot grpmax-eligible | 0.144% | 692 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0676% | 1,479 |
| Admixed American | 0.0417% | 2,399 |
| European (non-Finnish) | 0.0282% | 3,549 |
| Finnishnot grpmax-eligible | 0.00937% | 10,668 |
| African / African-American | 0.00933% | 10,718 |
| East Asian | 0.00446% | 22,424 |
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.Ala38=
- Coding
- c.114A>G
- MANE Select
- NM_004311
- dbSNP
- rs139645455
- Type
- single nucleotide variant
- Location
- chr10:102705379 (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-ala38 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown