Is ABCA4 p.Phe213fs (c.639del) pathogenic?

ABCA4 p.Phe213fs (c.639del) is classified Pathogenic in ABCA4 (ClinVar, Single submitter, 1 submitter; last evaluated 2020-01-09). No gnomAD frequency available for this variant; Associated with cone-rod dystrophy.

What condition is associated with ABCA4 p.Phe213fs (c.639del)?

ABCA4 p.Phe213fs (c.639del) is associated with cone-rod dystrophy (ClinVar).

How common is ABCA4 p.Phe213fs (c.639del) in the general population?

ABCA4 p.Phe213fs (c.639del) is no gnomAD frequency available for this variant (gnomAD).

How is Cone rod dystrophy inherited?

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

ABCA4 p.Phe213fs

c.639del · rs1662213462 · VCV813143

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

Conditions

cone-rod 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 6 of 50
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -0.41	GERP -3.8, phastCons 0.092

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.Phe213fs
Coding: c.639del
MANE Select: NM_000350
dbSNP: rs1662213462
Type: Deletion
Location: chr1:94098923 (GRCh38)
Gene constraint: LOEUF 0.786 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 75.96 · 8 PDB
Residue 213: a UniProt-annotated variant site (in cord3; uncertain significance); a UniProt-annotated variant site (in stgd1; uncertain significance); an α-helix

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

Disease context

cone-rod dystrophy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Cone rod dystrophy (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, X-linked recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

ABCA4 p.Arg1843_Gly1844del Pathogenic/Likely pathogenic ★★ same condition
ABCA4 p.Val1682_Val1686del Pathogenic ★★ same condition
ABCA4 p.Phe213Tyr Uncertain significance ★★ ⚠ same residue
ABCA4 p.Ala116fs Pathogenic ★ same condition
ABCA4 p.Phe213Leu Uncertain significance ★ ⚠ same residue
ABCA4 c.5196+1137G>A Pathogenic ★★★ same condition
ABCA4 c.5714+5G>A Pathogenic ★★★ same condition
ABCA4 p.Arg2107His 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-phe213fs (accessed [today's date]).

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