Is ACTC1 p.Leu106Val (c.316C>G) pathogenic?

ACTC1 p.Leu106Val (c.316C>G) is classified Uncertain significance in ACTC1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-07-04). AlphaMissense: likely pathogenic (0.745); Absent from gnomAD v4.1.

How common is ACTC1 p.Leu106Val (c.316C>G) in the general population?

ACTC1 p.Leu106Val (c.316C>G) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about ACTC1 p.Leu106Val (c.316C>G)?

AlphaMissense predicts likely pathogenic (score 0.745) — an in-silico prediction, not a clinical call.

ACTC1 p.Leu106Val

c.316C>G · VCV3393779

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.745 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

3/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.745	likely pathogenic
REVEL	0.814	moderately pathogenic-leaning
SaProt	LLR -13.34	damaging
⇒ AlphaMissense, REVEL and SaProt all call this damaging.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 4.1	GERP 2.3, phastCons 1
Regional constraint	o/e 0.34	constrained · MANE · 1,330 bp · p 2.8e-11 · regional, not allelic
Overall
CADD	25.0	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — 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

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: ACTC1
Protein: p.Leu106Val
Coding: c.316C>G
MANE Select: NM_005159
Type: single nucleotide variant
Location: chr15:34793383 (GRCh38)
Gene constraint: LOEUF 0.511 · pLI 0.97 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 95.47 · 16 PDB
Residue 106: a β-strand

Full ACTC1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ACTC1 p.Leu106= Likely benign ★ same residue
ACTC1 p.Glu101Lys Pathogenic ★★★ same type
ACTC1 p.Gly345Val Uncertain significance ★★★ ⚠ same type
ACTC1 p.Pro266Leu Uncertain significance ★★★ ⚠ same type
ACTC1 p.Val56Ile Uncertain significance ★★★ ⚠ same type
ACTC1 p.Ala297Ser Pathogenic ★★ ⚠ same type
ACTC1 p.Gly247Asp Pathogenic/Likely pathogenic ★★ same type
ACTC1 p.Thr128Ile Likely pathogenic ★★ 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/actc1-p-leu106val (accessed [today's date]).

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