Is ACTB p.Lys118del (c.350AGA[1]) pathogenic?

ACTB p.Lys118del (c.350AGA[1]) is classified Uncertain significance in ACTB (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-19). Absent from gnomAD; Associated with neurodevelopmental disorder.

What condition is associated with ACTB p.Lys118del (c.350AGA[1])?

ACTB p.Lys118del (c.350AGA[1]) is associated with neurodevelopmental disorder (ClinVar).

How common is ACTB p.Lys118del (c.350AGA[1]) in the general population?

ACTB p.Lys118del (c.350AGA[1]) is absent from gnomAD (gnomAD).

ACTB p.Lys118del

c.350AGA[1] · rs2533849974 · VCV2627879

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

neurodevelopmental disorder

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 9.3	GERP 2.1, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: ACTB
Protein: p.Lys118del
Coding: c.350AGA[1]
MANE Select: NM_001101
dbSNP: rs2533849974
Type: Microsatellite
Location: chr7:5529169 (GRCh38)
Gene constraint: LOEUF 0.193 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 95.31 · 93 PDB
Residue 118: an α-helix

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

Disease context

neurodevelopmental disorder — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACTB p.Lys118_Met119delinsMetThr Pathogenic ★ same residue
ACTB p.Lys118Arg Uncertain significance ★ same residue
ACTB p.Lys118= Likely benign ★ same residue
ACTB p.Asp11del Likely pathogenic ★ same condition
ACTB p.Asp56Tyr Likely pathogenic ★ same condition
ACTB p.Gln360fs Likely pathogenic ★ same condition
ACTB p.Val219Ile Likely pathogenic ★ ⚠ same condition
ACTB p.Thr297fs 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/actb-p-lys118del (accessed [today's date]).

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