Is ABCA3 p.His904fs (c.2708dup) pathogenic?

ABCA3 p.His904fs (c.2708dup) is classified Pathogenic in ABCA3 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-04-17). Absent from gnomAD.

How common is ABCA3 p.His904fs (c.2708dup) in the general population?

ABCA3 p.His904fs (c.2708dup) is absent from gnomAD (gnomAD).

ABCA3 p.His904fs

c.2708dup · rs2505627637 · VCV2857174

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

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 21 of 33
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.23	GERP -5.1, phastCons 0.027

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

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. 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.His904fs
Coding: c.2708dup
MANE Select: NM_001089
dbSNP: rs2505627637
Type: Duplication
Location: chr16:2288321 (GRCh38)
Gene constraint: LOEUF 0.612 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 81.00 · 2 PDB
Residue 904: an α-helix

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

Similar variants

ABCA3 p.Asp731fs Pathogenic/Likely pathogenic ★★ same type
ABCA3 p.Tyr492fs Pathogenic/Likely pathogenic ★★ same type
ABCA3 p.Val1303fs Pathogenic ★★ same type
ABCA3 c.873+84dup Benign ★★ same type
ABCA3 p.Ala1629fs Likely pathogenic ★ same type
ABCA3 p.Asn1020Ter Pathogenic ★ same type
ABCA3 p.Asn1519fs Likely pathogenic ★ same type
ABCA3 p.Gly429fs 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-his904fs (accessed [today's date]).

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