ARL6 p.Phe128=
c.384T>C · rs2529973628 · VCV2939899
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Bardet-Biedl syndrome 3
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.258 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.9 | GERP -0.44, phastCons 1 |
| Overall | ||
| CADD | 8.858 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- ARL6
- Protein
- p.Phe128=
- Coding
- c.384T>C
- MANE Select
- NM_001278293
- dbSNP
- rs2529973628
- Type
- single nucleotide variant
- Location
- chr3:97788024 (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 128
- a β-strand
Disease context
Bardet-Biedl syndrome 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: retinitis pigmentosa 55
For Bardet-Biedl syndrome (Orphanet):
- Inheritance
- Autosomal recessive, Oligogenic
- Onset
- Antenatal, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Specific population)
Similar variants
- ARL6 c.185+1G>C Pathogenic ★★ same condition
- ARL6 c.255-2A>T Pathogenic ★★ same condition
- ARL6 c.349+1G>A Likely pathogenic ★★ same condition
- ARL6 c.350-2A>C Pathogenic/Likely pathogenic ★★ same condition
- ARL6 p.Arg121His Pathogenic/Likely pathogenic ★★ ⚠ same condition
- ARL6 p.Arg122Ter Pathogenic ★★ same condition
- ARL6 p.Gln178= Pathogenic/Likely pathogenic ★★ same condition
- ARL6 p.Gly169Ala Pathogenic/Likely pathogenic ★★ 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-phe128 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown