OFD1 p.Arg60=
c.178C>A · rs758996532 · VCV2934459
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000224%, nfe)
Conditions
2
Joubert syndrome
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 0.99 | GERP -0.34 |
| Overall | ||
| CADD | 11.15 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000224%
European (non-Finnish) · 2/894,306 alleles
Filtering AF
3.7e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000165%
2/1,210,423 alleles · very rare
exomes 2/1,096,859 · genomes 0/113,564 · 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
- OFD1
- Protein
- p.Arg60=
- Coding
- c.178C>A
- MANE Select
- NM_003611
- dbSNP
- rs758996532
- Type
- single nucleotide variant
- Location
- chrX:13736544 (GRCh38)
- Structure
- AlphaFold pLDDT 68.41
Similar variants
- OFD1 p.Arg60Trp Uncertain significance ★★ ⚠ same residue
- OFD1 p.Arg60Gln Uncertain significance ★ ⚠ same residue
- OFD1 c.1411+1G>A Pathogenic ★★ same condition
- OFD1 c.2600-1G>C Pathogenic/Likely pathogenic ★★ same condition
- OFD1 p.Arg367Ter Pathogenic ★★ same condition
- OFD1 p.Arg41Ter Pathogenic ★★ same condition
- OFD1 p.Arg890Ter Pathogenic/Likely pathogenic ★★ same condition
- OFD1 p.Arg909Ter 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/ofd1-p-arg60 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown