ARL13B p.Pro46=
c.138T>C · VCV3628680
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.48e-05%, nfe)
Conditions
1
Joubert syndrome 8
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 0.87 | GERP -0.46, phastCons 1 |
| Overall | ||
| CADD | 9.912 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.48e-05%
European (non-Finnish) · 1/1,179,468 alleles
Overall
6.2e-05%
1/1,613,098 alleles · very rare
exomes 0/1,460,944 · genomes 1/152,154 · joint denominator
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
- ARL13B
- Protein
- p.Pro46=
- Coding
- c.138T>C
- MANE Select
- NM_001174150
- Type
- single nucleotide variant
- Location
- chr3:94003666 (GRCh38)
- Gene constraint
- LOEUF 0.894 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 72.92
Similar variants
- ARL13B c.1141+1G>A Likely pathogenic ★★ same condition
- ARL13B c.131-1G>T Pathogenic/Likely pathogenic ★★ same condition
- ARL13B p.Arg200Cys Pathogenic/Likely pathogenic ★★ same condition
- ARL13B p.Cys287Ter Pathogenic/Likely pathogenic ★★ same condition
- ARL13B p.Gln258Ter Pathogenic/Likely pathogenic ★★ same condition
- ARL13B p.Gly75Arg Pathogenic ★★ same condition
- ARL13B c.1211-1G>C Uncertain significance ★★ same condition
- ARL13B p.Ala210Val 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/arl13b-p-pro46 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown