Is ACTB p.Asp3Phe (c.7_8delinsTT) pathogenic?

ACTB p.Asp3Phe (c.78delinsTT) is classified Likely pathogenic in ACTB (ClinVar, Single submitter, 1 submitter; last evaluated 2019-08-07). Absent from gnomAD; Associated with Baraitser-Winter syndrome 1.

What condition is associated with ACTB p.Asp3Phe (c.7_8delinsTT)?

ACTB p.Asp3Phe (c.7_8delinsTT) is associated with Baraitser-Winter syndrome 1 (ClinVar).

How common is ACTB p.Asp3Phe (c.7_8delinsTT) in the general population?

ACTB p.Asp3Phe (c.7_8delinsTT) is absent from gnomAD (gnomAD).

ACTB p.Asp3Phe

c.7_8delinsTT · rs1784841235 · VCV968546

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Baraitser-Winter syndrome 1

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 5.9	GERP 2.1, phastCons 1
Regional constraint	o/e 0.12	constrained · MANE · 289 bp · p 4.5e-15 · regional, not allelic
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.Asp3Phe
Coding: c.7_8delinsTT
MANE Select: NM_001101
dbSNP: rs1784841235
Type: Indel
Location: chr7:5529650 (GRCh38)
Gene constraint: LOEUF 0.193 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 95.31 · 93 PDB
Residue 3: a turn

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

Disease context

Baraitser-Winter syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

ACTB c.364-17_364-16delinsTC Uncertain significance ★ same condition
ACTB p.Asp3His Uncertain significance ★ ⚠ same residue
ACTB c.364-16_364-15delinsCG Likely benign ★ same condition
ACTB c.985-17_985-16delinsAT Likely benign ★ same condition
ACTB p.Ala22Thr Likely pathogenic ★★ same condition
ACTB p.Ala7Thr Likely pathogenic ★★ same condition
ACTB p.Arg147Cys Pathogenic ★★ same condition
ACTB p.Arg183Trp 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/actb-p-asp3phe (accessed [today's date]).

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