OFD1 p.Lys237=
c.711G>A · VCV4948911
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0232%, mid)
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 0.039 | GERP -4.8, phastCons 0.001 |
| Overall | ||
| CADD | 0.627 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0232%
Middle Eastern · 1/4,311 alleles
Filtering AF
0.000596%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000223%
Overall
0.000333%
4/1,200,676 alleles · ultra-rare
exomes 4/1,087,653 · genomes 0/113,023 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0232% | 4,311 |
| South Asian | 0.00359% | 27,844 |
| European (non-Finnish) | 0.000113% | 887,351 |
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.Lys237=
- Coding
- c.711G>A
- MANE Select
- NM_003611
- Type
- single nucleotide variant
- Location
- chrX:13746836 (GRCh38)
- Structure
- AlphaFold pLDDT 68.41
Similar variants
- OFD1 p.Lys237Arg Uncertain significance ★ ⚠ same residue
- OFD1 p.Lys237fs Pathogenic ★★ same residue
- OFD1 c.1411+1G>A Pathogenic ★★ same type
- OFD1 c.2600-1G>C Pathogenic/Likely pathogenic ★★ same type
- OFD1 c.655-8A>G Likely pathogenic ★★ same type
- OFD1 p.Arg367Ter Pathogenic ★★ same type
- OFD1 p.Arg41Ter Pathogenic ★★ same type
- OFD1 p.Arg890Ter Pathogenic/Likely pathogenic ★★ same type
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-lys237 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown