ARL6 p.Val18=
c.54T>A · VCV3347806
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00111%, nfe)
Conditions
1
ARL6-related disorder
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 2.9 | GERP 0.91, phastCons 1 |
| Overall | ||
| CADD | 10.4 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00111%
European (non-Finnish) · 13/1,174,872 alleles
Filtering AF
0.000617%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000476%
Overall
0.000893%
13/1,456,172 alleles · very rare
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
- ARL6
- Protein
- p.Val18=
- Coding
- c.54T>A
- MANE Select
- NM_001278293
- Type
- single nucleotide variant
- Location
- chr3:97768161 (GRCh38)
- Gene constraint
- LOEUF 0.956 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 94.81 · 1 PDB
- Residue 18
- a β-strand
Disease context
ARL6-related disorder
Similar variants
- ARL6 p.Val18Ile Uncertain significance ★★ ⚠ same residue
- ARL6 c.185+1G>C Pathogenic ★★ same condition
- ARL6 p.Gly169Ala Pathogenic/Likely pathogenic ★★ same condition
- ARL6 p.Ile91Thr Pathogenic/Likely pathogenic ★★ same condition
- ARL6 p.Thr31Arg Pathogenic/Likely pathogenic ★★ same condition
- ARL6 p.Thr31Met Pathogenic/Likely pathogenic ★★ same condition
- ARL6 p.Trp176Cys Pathogenic/Likely pathogenic ★★ same condition
- ARL6 p.Ser40Ala Uncertain significance ★ ⚠ same condition
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/arl6-p-val18 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown