Is ABCA3 p.Asp507fs (c.1521_1522del) pathogenic?

ABCA3 p.Asp507fs (c.15211522del) is classified Likely pathogenic in ABCA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-06-01). Associated with interstitial lung disease due to ABCA3 deficiency.

What condition is associated with ABCA3 p.Asp507fs (c.1521_1522del)?

ABCA3 p.Asp507fs (c.1521_1522del) is associated with interstitial lung disease due to ABCA3 deficiency (ClinVar).

ABCA3 p.Asp507fs

Q: How is Interstitial lung disease due to ABCA3 deficiency inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

c.1521_1522del · VCV3580026

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

interstitial lung disease due to ABCA3 deficiency

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 13 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 0.62	GERP -2.7

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

Variant & gene context

Gene: ABCA3
Protein: p.Asp507fs
Coding: c.1521_1522del
MANE Select: NM_001089
Type: Deletion
Location: chr16:2300094 (GRCh38)
Gene constraint: LOEUF 0.612 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.00 · 2 PDB

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

Disease context

interstitial lung disease due to ABCA3 deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Interstitial lung disease due to ABCA3 deficiency (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy, Neonatal

Similar variants

ABCA3 p.Leu1584fs Likely pathogenic ★★ same condition
ABCA3 p.Tyr273fs Pathogenic ★★ same condition
ABCA3 c.1467+1903_1612-126del Pathogenic ★ same condition
ABCA3 p.Asp1058fs Likely pathogenic ★ same condition
ABCA3 p.Cys1256fs Likely pathogenic ★ same condition
ABCA3 p.Gly1444fs Likely pathogenic ★ same condition
ABCA3 p.Trp1554fs Likely pathogenic ★ same condition
ABCA3 c.2513+311del Uncertain significance ★ 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/abca3-p-asp507fs (accessed [today's date]).

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