Is OTC p.Pro319del (c.953CTC[1]) pathogenic?

OTC p.Pro319del (c.953CTC[1]) is classified Uncertain significance in OTC (ClinVar, Multiple submitters, 2 submitters; last evaluated 2019-09-13). No gnomAD frequency available for this variant; Associated with Inborn genetic diseases.

What condition is associated with OTC p.Pro319del (c.953CTC[1])?

OTC p.Pro319del (c.953CTC[1]) is associated with Inborn genetic diseases, ornithine carbamoyltransferase deficiency (ClinVar).

How common is OTC p.Pro319del (c.953CTC[1]) in the general population?

OTC p.Pro319del (c.953CTC[1]) is no gnomAD frequency available for this variant (gnomAD).

OTC p.Pro319del

c.953CTC[1] · rs1555976710 · VCV521440

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Inborn genetic diseases

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.8	GERP 2.2, phastCons 1

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: OTC
Protein: p.Pro319del
Coding: c.953CTC[1]
MANE Select: NM_000531
dbSNP: rs1555976710
Type: Microsatellite
Location: chrX:38411947 (GRCh38)
Structure: AlphaFold pLDDT 91.94 · 4 PDB

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

Disease context

Inborn genetic diseases — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: ornithine carbamoyltransferase deficiency

Similar variants

OTC p.Pro319Ser Uncertain significance ★ ⚠ same residue
OTC p.Glu310del Pathogenic ★★ same condition
OTC c.217-5TA[4] Likely benign ★★ same condition
OTC p.Arg89fs Likely pathogenic ★ same condition
OTC p.Glu273del Likely pathogenic ★ same condition
OTC p.Arg89del Uncertain significance ★ same condition
OTC c.298+2T>G Pathogenic ★★ same condition
OTC c.299-1G>A 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/otc-p-pro319del (accessed [today's date]).

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