OFD1 p.Arg836=
c.2508G>A · rs2048023499 · VCV1956498
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.000335%, 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 0.83 | GERP 0.06 |
| Overall | ||
| CADD | 0.984 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000335%
European (non-Finnish) · 3/894,724 alleles
Filtering AF
8.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.5e-05%
Overall
0.000248%
3/1,210,843 alleles · very rare
exomes 3/1,097,020 · genomes 0/113,823 · 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.Arg836=
- Coding
- c.2508G>A
- MANE Select
- NM_003611
- dbSNP
- rs2048023499
- Type
- single nucleotide variant
- Location
- chrX:13763764 (GRCh38)
- Structure
- AlphaFold pLDDT 68.41
- Residue 836
- the 'mediates the interaction with sdccag8' region; the 'disordered' region
Similar variants
- 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
- OFD1 p.Tyr87Cys Pathogenic ★★ ⚠ same condition
- OFD1 c.2388-3T>C 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/ofd1-p-arg836 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown