OFD1 p.Ala678=
c.2034C>T · VCV4948955
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00202%, sas)
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 -1.6 | GERP -4.3 |
| Overall | ||
| CADD | 0.335 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00202%
South Asian · 1/49,476 alleles
Filtering AF
3.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.4e-05%
Overall
0.000257%
3/1,167,817 alleles · very rare
exomes 3/1,054,137 · genomes 0/113,680 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00202% | 49,476 |
| European (non-Finnish) | 0.000228% | 438,172 |
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.Ala678=
- Coding
- c.2034C>T
- MANE Select
- NM_003611
- Type
- single nucleotide variant
- Location
- chrX:13760494 (GRCh38)
- Structure
- AlphaFold pLDDT 68.41
- Residue 678
- the 'mediates the interaction with sdccag8' region
Similar variants
- OFD1 p.Ala678Gly Benign/Likely benign ★★ 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
- OFD1 p.Arg909Ter 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-ala678 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown