Is OXCT1 p.Ser378= (c.1134T>C) pathogenic?

OXCT1 p.Ser378= (c.1134T>C) is classified Likely benign in OXCT1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-12). Absent from gnomAD v4.1; Associated with succinyl-CoA:3-ketoacid CoA transferase deficiency.

What condition is associated with OXCT1 p.Ser378= (c.1134T>C)?

OXCT1 p.Ser378= (c.1134T>C) is associated with succinyl-CoA:3-ketoacid CoA transferase deficiency (ClinVar).

How common is OXCT1 p.Ser378= (c.1134T>C) in the general population?

OXCT1 p.Ser378= (c.1134T>C) is absent from gnomAD v4.1 (gnomAD).

OXCT1 p.Ser378=

Q: How is Succinyl-CoA:3-oxoacid CoA transferase deficiency inherited?

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

c.1134T>C · VCV3692345

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

succinyl-CoA:3-ketoacid CoA transferase deficiency

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	all four deltas below 0.2 · A>C here scores Δ0.26 · evaluated, not missing
Constraint at this position
Conservation	phyloP 2.8	GERP 0.54, phastCons 1
Overall
CADD	14.28	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: OXCT1
Protein: p.Ser378=
Coding: c.1134T>C
MANE Select: NM_000436
Type: single nucleotide variant
Location: chr5:41794715 (GRCh38)
Gene constraint: LOEUF 0.521 · pLI 0.97 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.33 · 1 PDB
Residue 378: a UniProt-annotated variant site (in scotd); a β-strand

Full OXCT1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

succinyl-CoA:3-ketoacid CoA transferase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Succinyl-CoA:3-oxoacid CoA transferase deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal

Similar variants

OXCT1 c.1099+2T>C Likely pathogenic ★★ same condition
OXCT1 c.278+1G>A Likely pathogenic ★★ same condition
OXCT1 p.Arg124Ter Likely pathogenic ★★ same condition
OXCT1 p.Arg468Cys Pathogenic/Likely pathogenic ★★ ⚠ same condition
OXCT1 c.671+3A>G Uncertain significance ★★ same condition
OXCT1 p.Ala401Val Uncertain significance ★★ ⚠ same condition
OXCT1 p.Ala519Thr Uncertain significance ★★ ⚠ same condition
OXCT1 p.Arg110His Uncertain significance ★★ ⚠ 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/oxct1-p-ser378 (accessed [today's date]).

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