Is ACTB p.Asp56= (c.168C>T) pathogenic?

ACTB p.Asp56= (c.168C>T) is classified Benign/Likely benign in ACTB (ClinVar, Multiple submitters, 9 submitters; last evaluated 2026-03-01). Rare (popmax 0.477%, afr); Associated with Baraitser-Winter syndrome 1.

What condition is associated with ACTB p.Asp56= (c.168C>T)?

ACTB p.Asp56= (c.168C>T) is associated with Baraitser-Winter syndrome 1, developmental malformations-deafness-dystonia syndrome (ClinVar).

How common is ACTB p.Asp56= (c.168C>T) in the general population?

ACTB p.Asp56= (c.168C>T) is rare (popmax 0.477%, afr) (gnomAD).

ACTB p.Asp56=

c.168C>T · rs13447398 · VCV290840

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 9 submitters

gnomAD v4.1

Rare

rare (popmax 0.477%, afr)

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 · no allele here is in the release
Constraint at this position
Conservation	phyloP -3.7	GERP -4.3
Overall
CADD	1.582	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.477% African / African-American · 358/75,062 alleles

Filtering AF 0.436% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.42%

Overall 0.0311% 502/1,614,052 alleles · rare exomes 285/1,461,704 · genomes 217/152,348 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.477%	210
Middle Eastern	0.066%	1,516
Admixed American	0.0533%	1,876
Remaining individualsnot grpmax-eligible	0.0496%	2,016
South Asian	0.00878%	11,386
European (non-Finnish)	0.00585%	17,102

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: ACTB
Protein: p.Asp56=
Coding: c.168C>T
MANE Select: NM_001101
dbSNP: rs13447398
Type: single nucleotide variant
Location: chr7:5529356 (GRCh38)
Gene constraint: LOEUF 0.193 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
Structure: AlphaFold pLDDT 95.31 · 93 PDB
Residue 56: an α-helix

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

Also linked: developmental malformations-deafness-dystonia syndrome

Similar variants

ACTB p.Asp56Asn Likely pathogenic ★ same residue
ACTB p.Asp56Tyr Likely pathogenic ★ same residue
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
ACTB p.Arg196Cys Pathogenic ★★ same condition
ACTB p.Arg196His 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-asp56 (accessed [today's date]).

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