Is ACACB p.Pro43Leu (c.128C>T) pathogenic?

ACACB p.Pro43Leu (c.128C>T) is classified Likely benign in ACACB (ClinVar, Single submitter, 2 submitters; last evaluated 2024-01-12). AlphaMissense: likely benign (0.0677); Rare (popmax 0.231%, afr).

How common is ACACB p.Pro43Leu (c.128C>T) in the general population?

ACACB p.Pro43Leu (c.128C>T) is rare (popmax 0.231%, afr) (gnomAD).

What do computational predictors say about ACACB p.Pro43Leu (c.128C>T)?

AlphaMissense predicts likely benign (score 0.0677) — an in-silico prediction, not a clinical call.

ACACB p.Pro43Leu

c.128C>T · rs142445607 · VCV3133603

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.0677 · ACMG-weighted

gnomAD v4.1

Rare

rare (popmax 0.231%, afr)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0677	likely benign
REVEL	0.283	benign-leaning
SaProt	LLR -6.53	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 -5.3
Regional constraint	o/e 0.88	unconstrained · MANE · 111 kb · p 4.8e-09 · regional, not allelic
Overall
CADD	0.034	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 0.231% African / African-American · 173/75,014 alleles

Filtering AF 0.203% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.192%

Overall 0.0137% 221/1,614,126 alleles · rare exomes 111/1,461,892 · genomes 110/152,234 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.231%	434
Admixed American	0.04%	2,500
Remaining individualsnot grpmax-eligible	0.0144%	6,945
East Asian	0.00223%	44,888
South Asian	0.0022%	45,536
European (non-Finnish)	0.00102%	98,336

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: ACACB
Protein: p.Pro43Leu
Coding: c.128C>T
MANE Select: NM_001093
dbSNP: rs142445607
Type: single nucleotide variant
Location: chr12:109139533 (GRCh38)
Gene constraint: LOEUF 0.843 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.29 · 11 PDB
Residue 43: the 'disordered' region

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

Similar variants

ACACB p.Pro43= Likely benign same residue
ACACB p.Val958Met Uncertain significance ★★ ⚠ same type
ACACB c.6942+9C>T Benign ★★ same type
ACACB c.6943-8G>A Benign ★★ same type
ACACB c.7113+7C>T Benign/Likely benign ★★ same type
ACACB p.Ala650= Likely benign ★★ same type
ACACB p.Arg1786Gln Likely benign ★★ same type
ACACB p.Asp1481Val Benign/Likely benign ★★ same type

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/acacb-p-pro43leu (accessed [today's date]).

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