Is PC p.Arg1158His (c.3473G>A) pathogenic?

PC p.Arg1158His (c.3473G>A) is classified Uncertain significance in PC (ClinVar, Multiple submitters, 4 submitters; last evaluated 2022-09-07). AlphaMissense: likely benign (0.098); Ultra-rare (popmax 0.0277%, nfe); Associated with pyruvate carboxylase deficiency disease.

What condition is associated with PC p.Arg1158His (c.3473G>A)?

PC p.Arg1158His (c.3473G>A) is associated with pyruvate carboxylase deficiency disease (ClinVar).

How common is PC p.Arg1158His (c.3473G>A) in the general population?

PC p.Arg1158His (c.3473G>A) is ultra-rare (popmax 0.0277%, nfe) (gnomAD).

How is Pyruvate carboxylase deficiency inherited?

Typically Autosomal recessive, Not applicable (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about PC p.Arg1158His (c.3473G>A)?

AlphaMissense predicts likely benign (score 0.098) — an in-silico prediction, not a clinical call.

PC p.Arg1158His

c.3473G>A · rs149054698 · VCV305615

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

AlphaMissense

likely benign

0.098 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0277%, nfe)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

pyruvate carboxylase deficiency disease

Computational evidence

Protein change
AlphaMissense	0.098	likely benign
REVEL	0.069	moderately benign-leaning
SaProt	LLR -7.24	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.56	GERP -0.42, phastCons 0.99
Regional constraint	o/e 1.07	unconstrained · MANE · 198 bp · p 0.48 · regional, not allelic
Overall
CADD	23.3	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean tolerated — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0277% European (non-Finnish) · 327/1,180,016 alleles

Filtering AF 0.0252% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0242%

Overall 0.0215% 347/1,613,930 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0277%	3,609
Remaining individualsnot grpmax-eligible	0.0144%	6,943
Admixed American	0.00667%	15,002
African / African-American	0.00534%	18,734
East Asian	0.00223%	44,898
Finnishnot grpmax-eligible	0.00157%	63,894
South Asian	0.0011%	91,090

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: PC
Protein: p.Arg1158His
Coding: c.3473G>A
MANE Select: NM_001040716
dbSNP: rs149054698
Type: single nucleotide variant
Location: chr11:66848963 (GRCh38)
Gene constraint: LOEUF 0.539 · pLI 0.07 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.53 · 10 PDB
Residue 1158: the biotinyl-binding domain

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

Disease context

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

For Pyruvate carboxylase deficiency (Orphanet):

Inheritance: Autosomal recessive, Not applicable
Onset: Infancy, Neonatal
Prevalence: 1-9 / 1 000 000 (Europe)

Similar variants

PC p.Arg1158= Likely benign ★ same residue
PC p.Arg1158Cys Uncertain significance ★ ⚠ same residue
PC c.1368+1G>A Likely pathogenic ★★ same condition
PC c.1826-1G>C Likely pathogenic ★★ same condition
PC c.1983-116C>T Likely pathogenic ★★ same condition
PC c.633+2T>C Likely pathogenic ★★ same condition
PC p.Ala610Thr Pathogenic ★★ same condition
PC p.Ala812Asp 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/pc-p-arg1158his (accessed [today's date]).

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