Is PC p.Gly89Ser (c.265G>A) pathogenic?

PC p.Gly89Ser (c.265G>A) is classified Uncertain significance in PC (ClinVar, Single submitter, 1 submitter; last evaluated 2024-12-07). AlphaMissense: likely benign (0.2095); Ultra-rare (popmax 0.0208%, eas); Associated with pyruvate carboxylase deficiency disease.

What condition is associated with PC p.Gly89Ser (c.265G>A)?

PC p.Gly89Ser (c.265G>A) is associated with pyruvate carboxylase deficiency disease (ClinVar).

How common is PC p.Gly89Ser (c.265G>A) in the general population?

PC p.Gly89Ser (c.265G>A) is ultra-rare (popmax 0.0208%, eas) (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.Gly89Ser (c.265G>A)?

AlphaMissense predicts likely benign (score 0.2095) — an in-silico prediction, not a clinical call.

PC p.Gly89Ser

c.265G>A · VCV3702636

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2095 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0208%, eas)

Missense predictors

1/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

pyruvate carboxylase deficiency disease

Computational evidence

Protein change
AlphaMissense	0.2095	likely benign
REVEL	0.767	pathogenic-leaning
SaProt	LLR -9.99	tolerated
⇒ REVEL calls this damaging; AlphaMissense and SaProt do not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.6	GERP 1.6, phastCons 1
Regional constraint	o/e 0.74	unconstrained · MANE · 23 kb · p 3.1e-25 · regional, not allelic
Overall
CADD	24.3	PHRED · no single calibrated threshold — expert panels disagree

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0208% East Asian · 9/43,192 alleles

Filtering AF 0.0109% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00806%

Overall 0.00126% 20/1,583,390 alleles · ultra-rare exomes 19/1,431,166 · genomes 1/152,224 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0208%	4,799
Admixed American	0.00363%	27,538
Remaining individualsnot grpmax-eligible	0.00326%	30,664
South Asian	0.00229%	43,656
European (non-Finnish)	0.000429%	233,010

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.Gly89Ser
Coding: c.265G>A
MANE Select: NM_001040716
Type: single nucleotide variant
Location: chr11:66871743 (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 89: the biotin carboxylation 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 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
PC p.Arg18Ter Pathogenic/Likely pathogenic ★★ same condition
PC p.Arg263Ter 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-gly89ser (accessed [today's date]).

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