Is ABCA3 p.Thr586fs (c.1755del) pathogenic?

ABCA3 p.Thr586fs (c.1755del) is classified Pathogenic in ABCA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-01-02). Absent from gnomAD v4.1.

How common is ABCA3 p.Thr586fs (c.1755del) in the general population?

ABCA3 p.Thr586fs (c.1755del) is absent from gnomAD v4.1 (gnomAD).

ABCA3 p.Thr586fs

c.1755del · rs2505642538 · VCV2736310

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,613,528)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 15 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 2.4	GERP 0.59, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,613,528). 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: ABCA3
Protein: p.Thr586fs
Coding: c.1755del
MANE Select: NM_001089
dbSNP: rs2505642538
Type: Deletion
Location: chr16:2298527 (GRCh38)
Gene constraint: LOEUF 0.612 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.00 · 2 PDB
Residue 586: the abc transporter 1 domain

Full ABCA3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCA3 p.Thr586= Likely benign ★ same residue
ABCA3 p.Arg1333fs Pathogenic ★★ same type
ABCA3 p.Leu1584fs Likely pathogenic ★★ same type
ABCA3 p.Tyr273fs Pathogenic ★★ same type
ABCA3 p.Val1495fs Pathogenic/Likely pathogenic ★★ same type
ABCA3 c.1285+4_1285+7del Likely pathogenic ★ same type
ABCA3 c.1467+1903_1612-126del Pathogenic ★ same type
ABCA3 p.Asp1058fs 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/abca3-p-thr586fs (accessed [today's date]).

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