Is PCCB p.Ala3Val (c.8C>T) pathogenic?

PCCB p.Ala3Val (c.8C>T) is classified Uncertain significance in PCCB (ClinVar, Multiple submitters, 2 submitters; last evaluated 2023-05-05). AlphaMissense: likely benign (0.1631); Ultra-rare (popmax 0.0165%, afr); Associated with Inborn genetic diseases.

What condition is associated with PCCB p.Ala3Val (c.8C>T)?

PCCB p.Ala3Val (c.8C>T) is associated with Inborn genetic diseases, propionic acidemia (ClinVar).

How common is PCCB p.Ala3Val (c.8C>T) in the general population?

PCCB p.Ala3Val (c.8C>T) is ultra-rare (popmax 0.0165%, afr) (gnomAD).

What do computational predictors say about PCCB p.Ala3Val (c.8C>T)?

AlphaMissense predicts likely benign (score 0.1631) — an in-silico prediction, not a clinical call.

PCCB p.Ala3Val

c.8C>T · rs373685372 · VCV1403866

Uncertain significance Multiple submitters

Classification

Uncertain significance

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1631 · ACMG-weighted

gnomAD v4.1

Rare

ultra-rare (popmax 0.0165%, afr)

Missense predictors

0/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

Inborn genetic diseases

Computational evidence

Protein change
AlphaMissense	0.1631	likely benign
REVEL	0.401	indeterminate
SaProt	LLR -8.82	tolerated
⇒ AlphaMissense and SaProt both call this tolerated; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.6	GERP 0.54, phastCons 0.98
Regional constraint	o/e 1.09	unconstrained · MANE · 80 kb · p 0.017 · regional, not allelic
Overall
CADD	21.0	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 0.0165% African / African-American · 12/72,608 alleles

Filtering AF 0.00949% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00743%

Overall 0.0019% 29/1,525,538 alleles · ultra-rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0165%	6,051
Remaining individualsnot grpmax-eligible	0.0017%	58,666
European (non-Finnish)	0.00141%	70,771

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: PCCB
Protein: p.Ala3Val
Coding: c.8C>T
MANE Select: NM_000532
dbSNP: rs373685372
Type: single nucleotide variant
Location: chr3:136250383 (GRCh38)
Gene constraint: LOEUF 0.843 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 93.59 · 24 PDB

Full PCCB 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: propionic acidemia

Similar variants

PCCB p.Ala3= Likely benign ★ same residue
PCCB c.1199-1G>A Pathogenic/Likely pathogenic ★★ same condition
PCCB c.1199-2A>G Pathogenic ★★ same condition
PCCB c.1398+1G>C Pathogenic/Likely pathogenic ★★ same condition
PCCB c.1398+1G>T Pathogenic/Likely pathogenic ★★ same condition
PCCB c.1498+2T>C Pathogenic ★★ same condition
PCCB c.1499-1G>C Pathogenic/Likely pathogenic ★★ same condition
PCCB c.183+1G>A Pathogenic/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/pccb-p-ala3val (accessed [today's date]).

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