OTC p.Ser156=
c.468C>T · VCV4949870
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0141%, 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 0.85 | GERP 0.51, phastCons 1 |
| Overall | ||
| CADD | 8.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0141%
South Asian · 8/56,623 alleles
Filtering AF
0.00695%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00507%
Overall
0.000668%
8/1,197,247 alleles · ultra-rare
exomes 8/1,083,671 · genomes 0/113,576 · 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
- OTC
- Protein
- p.Ser156=
- Coding
- c.468C>T
- MANE Select
- NM_000531
- Type
- single nucleotide variant
- Location
- chrX:38401356 (GRCh38)
- Structure
- AlphaFold pLDDT 91.94 · 4 PDB
Similar variants
- OTC c.298+2T>G Pathogenic ★★ same type
- OTC c.299-1G>A Likely pathogenic ★★ same type
- OTC c.386+1G>A Pathogenic ★★ same type
- OTC c.540+1G>A Pathogenic ★★ same type
- OTC c.540+1G>T Pathogenic ★★ same type
- OTC c.540+265G>A Pathogenic ★★ same type
- OTC c.663+1G>T Pathogenic ★★ same type
- OTC c.663+2T>C 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/otc-p-ser156 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown