Is OTC p.Ile160= (c.480C>T) pathogenic?

OTC p.Ile160= (c.480C>T) is classified Likely benign in OTC (ClinVar, Single submitter, 1 submitter; last evaluated 2021-02-20). Absent from gnomAD v4.1; Associated with ornithine carbamoyltransferase deficiency.

What condition is associated with OTC p.Ile160= (c.480C>T)?

OTC p.Ile160= (c.480C>T) is associated with ornithine carbamoyltransferase deficiency (ClinVar).

How common is OTC p.Ile160= (c.480C>T) in the general population?

OTC p.Ile160= (c.480C>T) is absent from gnomAD v4.1 (gnomAD).

How is Ornithine transcarbamylase deficiency inherited?

Typically X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

OTC p.Ile160=

c.480C>T · rs2147341370 · VCV1580018

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

ornithine carbamoyltransferase deficiency

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 2.7	GERP 2.4, phastCons 1
Overall
CADD	11.55	PHRED · no single calibrated threshold — expert panels disagree

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: OTC
Protein: p.Ile160=
Coding: c.480C>T
MANE Select: NM_000531
dbSNP: rs2147341370
Type: single nucleotide variant
Location: chrX:38401368 (GRCh38)
Structure: AlphaFold pLDDT 91.94 · 4 PDB
Residue 160: a β-strand; a UniProt-annotated variant site (in otcd)

Full OTC gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

ornithine carbamoyltransferase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Ornithine transcarbamylase deficiency (Orphanet):

Inheritance: X-linked recessive
Onset: All ages
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

OTC p.Ile160Met Likely pathogenic ★ same residue
OTC p.Ile160Phe Likely pathogenic ★ same residue
OTC p.Ile160Asn Pathogenic same residue
OTC p.Ile160Ser Pathogenic same residue
OTC p.Ile160Thr Pathogenic same residue
OTC c.298+2T>G Pathogenic ★★ same condition
OTC c.299-1G>A Likely pathogenic ★★ same condition
OTC c.386+1G>A 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/otc-p-ile160 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown