Is ABCA4 p.Ile1671fs (c.5012_5016del) pathogenic?

ABCA4 p.Ile1671fs (c.50125016del) is classified Pathogenic/Likely pathogenic in ABCA4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-05-17). Absent from gnomAD; Associated with age related macular degeneration 2.

What condition is associated with ABCA4 p.Ile1671fs (c.5012_5016del)?

ABCA4 p.Ile1671fs (c.5012_5016del) is associated with age related macular degeneration 2, severe early-childhood-onset retinal dystrophy, retinitis pigmentosa 19 (ClinVar).

How common is ABCA4 p.Ile1671fs (c.5012_5016del) in the general population?

ABCA4 p.Ile1671fs (c.5012_5016del) is absent from gnomAD (gnomAD).

ABCA4 p.Ile1671fs

c.5012_5016del · rs1571257754 · VCV801507

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

age related macular degeneration 2

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 35 of 50
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 4.1	GERP 0.81, 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: ABCA4
Protein: p.Ile1671fs
Coding: c.5012_5016del
MANE Select: NM_000350
dbSNP: rs1571257754
Type: Deletion
Location: chr1:94021242 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.96 · 8 PDB
Residue 1671: a UniProt-annotated variant site (in cord3; uncertain significance); a UniProt-annotated variant site (in stgd1; uncertain significance); a UniProt-annotated variant site (found in a patient with chorioretinal atrophy; uncertain significance); a UniProt-annotated variant site (found in a patient with macular dystrophy; uncertain significance); a UniProt-annotated variant site (in stgd1 and cord3; uncertain significance); a UniProt-annotated variant site (sequence variant); a UniProt-annotated variant site (in stgd1 and ffm; uncertain significance); an α-helix

Full ABCA4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Also linked: severe early-childhood-onset retinal dystrophy retinitis pigmentosa 19 cone-rod dystrophy 3

Similar variants

ABCA4 p.Asp279fs Pathogenic ★★★ same condition
ABCA4 p.Gly1972_Val1973insTer Pathogenic ★★★ same condition
ABCA4 p.Gly963fs Pathogenic ★★★ same condition
ABCA4 p.Leu296fs Pathogenic ★★★ same condition
ABCA4 c.6729+5_6729+19del Pathogenic/Likely pathogenic ★★ same condition
ABCA4 p.Asn1818fs Pathogenic/Likely pathogenic ★★ same condition
ABCA4 p.Asn96fs Pathogenic ★★ same condition
ABCA4 p.Asp1613fs 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/abca4-p-ile1671fs (accessed [today's date]).

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