OFD1 p.Arg367Ter
c.1099C>T · rs312262863 · VCV41056
Pathogenic
Multiple submitters
Classification
Pathogenic
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Joubert syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function in a haploinsufficient gene (ClinGen) |
|---|---|---|
| NMD | predicted | premature termination codon in exon 11 of 23 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Pangolin | Δ0.39 | loss · gain 0.01 · not in the SpliceAI release · independent |
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP 1.5, phastCons 0.37 |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
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
- OFD1
- Protein
- p.Arg367Ter
- Coding
- c.1099C>T
- MANE Select
- NM_003611
- dbSNP
- rs312262863
- Type
- single nucleotide variant
- Location
- chrX:13753411 (GRCh38)
- Structure
- AlphaFold pLDDT 68.41
Similar variants
- OFD1 p.Arg367Gln Uncertain significance ★★ ⚠ same residue
- OFD1 p.Arg367Pro Uncertain significance ★ ⚠ same residue
- OFD1 p.Arg367Gly Uncertain significance ★★ ⚠ same residue
- OFD1 c.1411+1G>A Pathogenic ★★ same condition
- OFD1 c.2600-1G>C Pathogenic/Likely 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-arg367ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown