Is OTC p.Arg141Ter (c.421C>T) pathogenic?

OTC p.Arg141Ter (c.421C>T) is classified Pathogenic in OTC (ClinVar, Single submitter, 3 submitters; last evaluated 2021-11-01). No allele count reported in gnomAD v4.1 (AN 1,201,980); Associated with ornithine carbamoyltransferase deficiency.

What condition is associated with OTC p.Arg141Ter (c.421C>T)?

OTC p.Arg141Ter (c.421C>T) is associated with ornithine carbamoyltransferase deficiency (ClinVar).

How common is OTC p.Arg141Ter (c.421C>T) in the general population?

OTC p.Arg141Ter (c.421C>T) is no allele count reported in gnomAD v4.1 (AN 1,201,980) (gnomAD).

How is Ornithine transcarbamylase deficiency inherited?

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

OTC p.Arg141Ter

c.421C>T · rs67960011 · VCV10988

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 3 submitters

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,201,980)

Conditions

ornithine carbamoyltransferase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	predicted	premature termination codon in exon 5 of 10
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 2.4, phastCons 1
Overall
CADD	38.0	PHRED · no single calibrated threshold — expert panels disagree

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,201,980). 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.Arg141Ter
Coding: c.421C>T
MANE Select: NM_000531
dbSNP: rs67960011
Type: single nucleotide variant
Location: chrX:38401309 (GRCh38)
Structure: AlphaFold pLDDT 91.94 · 4 PDB
Residue 141: a β-strand; a binding site; a UniProt-annotated variant site (in otcd); a UniProt-annotated variant site (in otcd; most common variant; loss of ornithine carbamoyltransferase activity; activity is 100-fold lower)

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.Arg141Gln Pathogenic ★★ same residue
OTC p.Arg141Pro Likely pathogenic ★ same residue
OTC p.Arg141= Likely benign ★ same residue
OTC p.Arg141Gly 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
OTC c.540+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-arg141ter (accessed [today's date]).

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