Is ABCA4 p.Val671fs (c.2012_2013del) pathogenic?

ABCA4 p.Val671fs (c.20122013del) is classified Pathogenic/Likely pathogenic in ABCA4 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2024-08-20). Absent from gnomAD; Associated with severe early-childhood-onset retinal dystrophy.

What condition is associated with ABCA4 p.Val671fs (c.2012_2013del)?

ABCA4 p.Val671fs (c.2012_2013del) is associated with severe early-childhood-onset retinal dystrophy, retinitis pigmentosa (ClinVar).

How common is ABCA4 p.Val671fs (c.2012_2013del) in the general population?

ABCA4 p.Val671fs (c.2012_2013del) is absent from gnomAD (gnomAD).

How is Severe early-childhood-onset retinal dystrophy inherited?

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

ABCA4 p.Val671fs

c.2012_2013del · rs1661098509 · VCV813129

Pathogenic/Likely pathogenic Multiple submitters

Classification

Pathogenic/Likely pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

severe early-childhood-onset retinal dystrophy

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 14 of 50
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.9	GERP 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: ABCA4
Protein: p.Val671fs
Coding: c.2012_2013del
MANE Select: NM_000350
dbSNP: rs1661098509
Type: Microsatellite
Location: chr1:94060684 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.96 · 8 PDB
Residue 671: 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); an α-helix; a disulfide bond

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

Disease context

severe early-childhood-onset retinal dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: retinitis pigmentosa

For Severe early-childhood-onset retinal dystrophy (Orphanet):

Inheritance: Autosomal recessive
Onset: Childhood, Infancy

Similar variants

ABCA4 p.Gly766del Pathogenic/Likely pathogenic ★★ same condition
ABCA4 p.Leu541fs Pathogenic/Likely pathogenic ★★ same condition
ABCA4 p.Phe1417del Pathogenic ★★ same condition
ABCA4 p.Ser2080fs Pathogenic/Likely pathogenic ★★ same condition
ABCA4 p.Ser34_Leu35del Pathogenic/Likely pathogenic ★★ same condition
ABCA4 p.Thr1346fs Pathogenic ★★ same condition
ABCA4 p.Cys1797_Ala1798insTer Pathogenic ★ same condition
ABCA4 p.Val1921fs 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/abca4-p-val671fs (accessed [today's date]).

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