Is ACP3 p.Leu6Val (c.16C>G) pathogenic?

ACP3 p.Leu6Val (c.16C>G) is classified Likely benign in ACP3 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-03-25). AlphaMissense: likely benign (0.0717); Absent from gnomAD v4.1.

How common is ACP3 p.Leu6Val (c.16C>G) in the general population?

ACP3 p.Leu6Val (c.16C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ACP3 p.Leu6Val (c.16C>G)?

AlphaMissense predicts likely benign (score 0.0717) — an in-silico prediction, not a clinical call.

ACP3 p.Leu6Val

c.16C>G · VCV3999743

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.0717 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.0717	likely benign
REVEL	0.013	strongly benign-leaning
SaProt	LLR -6.66	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 -0.71	GERP -2.5
Regional constraint	o/e 1.01	unconstrained · MANE · 39 kb · p 0.9 · regional, not allelic
Overall
CADD	0.213	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

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: ACP3
Protein: p.Leu6Val
Coding: c.16C>G
MANE Select: NM_001099
Type: single nucleotide variant
Location: chr3:132317472 (GRCh38)
Gene constraint: LOEUF 1.079 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.51 · 17 PDB

Full ACP3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACP3 p.Asp301Glu Benign ★★ same type
ACP3 p.Ala116Ser Uncertain significance ★ ⚠ same type
ACP3 p.Ala121Ser Uncertain significance ★ ⚠ same type
ACP3 p.Ala311Thr Uncertain significance ★ ⚠ same type
ACP3 p.Ala4Thr Uncertain significance ★ ⚠ same type
ACP3 p.Ala9Thr Uncertain significance ★ ⚠ same type
ACP3 p.Arg111Gln Uncertain significance ★ ⚠ same type
ACP3 p.Arg111Trp Uncertain significance ★ ⚠ 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/acp3-p-leu6val (accessed [today's date]).

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