Is ABCA3 p.Phe810fs (c.2429_2430del) pathogenic?

ABCA3 p.Phe810fs (c.24292430del) is classified Pathogenic in ABCA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-09-15). Very rare (popmax 0.000254%, nfe); Associated with ABCA3-related disorder.

What condition is associated with ABCA3 p.Phe810fs (c.2429_2430del)?

ABCA3 p.Phe810fs (c.2429_2430del) is associated with ABCA3-related disorder (ClinVar).

How common is ABCA3 p.Phe810fs (c.2429_2430del) in the general population?

ABCA3 p.Phe810fs (c.2429_2430del) is very rare (popmax 0.000254%, nfe) (gnomAD).

ABCA3 p.Phe810fs

c.2429_2430del · rs2505632878 · VCV2628386

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

very rare (popmax 0.000254%, nfe)

Conditions

ABCA3-related disorder

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 19 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -3.6	GERP -5.3

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

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.000254% European (non-Finnish) · 3/1,179,824 alleles

Filtering AF 6.8e-05% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.9e-05%

Overall 0.000186% 3/1,613,754 alleles · very rare exomes 3/1,461,484 · genomes 0/152,270 · joint denominator

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: ABCA3
Protein: p.Phe810fs
Coding: c.2429_2430del
MANE Select: NM_001089
dbSNP: rs2505632878
Type: Deletion
Location: chr16:2292223 (GRCh38)
Gene constraint: LOEUF 0.612 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.00 · 2 PDB
Residue 810: an α-helix

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

Disease context

ABCA3-related disorder

Similar variants

ABCA3 p.Leu1584fs Likely pathogenic ★★ same condition
ABCA3 p.Val1495fs Pathogenic/Likely pathogenic ★★ same condition
ABCA3 p.Phe1592fs Pathogenic ★ same condition
ABCA3 p.Glu292Val Pathogenic/Likely pathogenic ★★ ⚠ same condition
ABCA3 p.Phe1203del Pathogenic/Likely pathogenic ★★ same condition
ABCA3 p.Ser802fs Pathogenic ★★ same condition
ABCA3 p.Tyr492fs Pathogenic/Likely pathogenic ★★ same condition
ABCA3 p.Arg1583Trp Likely 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/abca3-p-phe810fs (accessed [today's date]).

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