Is ACTN1 p.Asp531Val (c.1592A>T) pathogenic?

ACTN1 p.Asp531Val (c.1592A>T) is classified Likely pathogenic in ACTN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2019-02-01). AlphaMissense: likely pathogenic (0.9986); Very rare (popmax 8.47e-05%, nfe); Associated with thrombocytopenia.

What condition is associated with ACTN1 p.Asp531Val (c.1592A>T)?

ACTN1 p.Asp531Val (c.1592A>T) is associated with thrombocytopenia (ClinVar).

How common is ACTN1 p.Asp531Val (c.1592A>T) in the general population?

ACTN1 p.Asp531Val (c.1592A>T) is very rare (popmax 8.47e-05%, nfe) (gnomAD).

What do computational predictors say about ACTN1 p.Asp531Val (c.1592A>T)?

AlphaMissense predicts likely pathogenic (score 0.9986) — an in-silico prediction, not a clinical call.

ACTN1 p.Asp531Val

c.1592A>T · rs1594758046 · VCV627246

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.9986 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 8.47e-05%, nfe)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL no call

Conditions

thrombocytopenia

Computational evidence

Protein change
AlphaMissense	0.9986	likely pathogenic ✓ concordant with ClinVar · top 7% in ACTN1
REVEL	0.562	indeterminate
SaProt	LLR -12.41	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL makes no call.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 7.9	phastCons 1
Regional constraint	o/e 0.60	unconstrained · MANE · 32 kb · p 3.7e-34 · regional, not allelic
Overall
CADD	30.0	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

Grpmax group 8.47e-05% European (non-Finnish) · 1/1,179,976 alleles

Overall 6.84e-05% 1/1,461,858 alleles · very rare

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: ACTN1
Protein: p.Asp531Val
Coding: c.1592A>T
MANE Select: NM_001130004
dbSNP: rs1594758046
Type: single nucleotide variant
Location: chr14:68884211 (GRCh38)
Gene constraint: LOEUF 0.331 · pLI 1.00 (gnomAD)
Structure: AlphaFold pLDDT 85.39 · 4 PDB
Residue 531: the 'interaction with ddn' region

Full ACTN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

Similar variants

ACTN1 p.Asp531delinsGluGlyProTrpSer Likely pathogenic ★ same residue
ACTN1 p.Arg46Trp Pathogenic/Likely pathogenic ★★ same condition
ACTN1 p.Ile139Val Uncertain significance ★★ ⚠ same condition
ACTN1 p.Gly910Arg Likely pathogenic ★ same condition
ACTN1 p.Asn590Lys Uncertain significance ★ ⚠ same condition
ACTN1 p.Asp534His Uncertain significance ★ ⚠ same condition
ACTN1 p.Ile218Val Uncertain significance ★ ⚠ same condition
ACTN1 p.Thr257Arg Conflicting classifications of pathogenicity ★ ⚠ 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/actn1-p-asp531val (accessed [today's date]).

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