Is ABCA12 p.Phe1080fs (c.3240del) pathogenic?

ABCA12 p.Phe1080fs (c.3240del) is classified Pathogenic in ABCA12 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-06-30). Absent from gnomAD.

How common is ABCA12 p.Phe1080fs (c.3240del) in the general population?

ABCA12 p.Phe1080fs (c.3240del) is absent from gnomAD (gnomAD).

ABCA12 p.Phe1080fs

c.3240del · rs2469277059 · VCV2872381

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 23 of 53
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	GERP 1.2, phastCons 1

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: ABCA12
Protein: p.Phe1080fs
Coding: c.3240del
MANE Select: NM_173076
dbSNP: rs2469277059
Type: Deletion
Location: chr2:214997749 (GRCh38)
Gene constraint: LOEUF 0.582 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 68.32
Residue 1080: a UniProt-annotated variant site (in arci4b)

Full ABCA12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

ABCA12 p.Asn528fs Pathogenic/Likely pathogenic ★★ same type
ABCA12 p.Ile1128fs Pathogenic/Likely pathogenic ★★ same type
ABCA12 p.Phe2286fs Pathogenic ★★ same type
ABCA12 p.Val2442fs Pathogenic ★★ same type
ABCA12 c.2683+2del Likely pathogenic ★ same type
ABCA12 c.5469_5472del Pathogenic ★ same type
ABCA12 c.6962+2del Likely pathogenic ★ same type
ABCA12 c.7541_7542+1del 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/abca12-p-phe1080fs (accessed [today's date]).

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