ARL3 p.Thr103=
c.309G>A · rs576741297 · VCV1579640
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00895%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.65 | donor gain · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -3.5 |
| Overall | ||
| CADD | 19.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00895%
East Asian · 4/44,698 alleles
Filtering AF
0.00299%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00181%
Overall
0.00113%
18/1,591,224 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00895% | 11,174 |
| African / African-American | 0.00405% | 24,703 |
| Admixed American | 0.00171% | 58,572 |
| Remaining individualsnot grpmax-eligible | 0.00163% | 61,534 |
| South Asian | 0.00112% | 88,984 |
| European (non-Finnish) | 0.000687% | 145,514 |
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.Thr103=
- Coding
- c.309G>A
- MANE Select
- NM_004311
- dbSNP
- rs576741297
- Type
- single nucleotide variant
- Location
- chr10:102689899 (GRCh38)
- Gene constraint
- LOEUF 0.557 · pLI 0.93 (gnomAD)
- Structure
- AlphaFold pLDDT 92.73
Similar variants
- ARL3 p.Thr103Met Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-thr103 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown