Is RDH12 c.69del pathogenic?

RDH12 c.69del is classified Likely pathogenic in RDH12 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-03-02). No gnomAD frequency available for this variant; Associated with Leber congenital amaurosis 13.

What condition is associated with RDH12 c.69del?

RDH12 c.69del is associated with Leber congenital amaurosis 13 (ClinVar).

How common is RDH12 c.69del in the general population?

RDH12 c.69del is no gnomAD frequency available for this variant (gnomAD).

How is Leber congenital amaurosis inherited?

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

RDH12 c.69del

rs2503792325 · VCV2678303

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Leber congenital amaurosis 13

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 11	GERP 2.4, phastCons 1
Non-coding constraint	Z 2.11	1 kb window · o/e 0.76 · regional · uncalibrated

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: RDH12
Coding: c.69del
MANE Select: NM_152443
dbSNP: rs2503792325
Type: Deletion
Location: chr14:67724472 (GRCh38)
Gene constraint: LOEUF 0.862 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 92.21

Full RDH12 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Leber congenital amaurosis 13 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Leber congenital amaurosis (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

RDH12 p.Ala166fs Pathogenic/Likely pathogenic ★★ same condition
RDH12 p.Ala64fs Pathogenic ★★ same condition
RDH12 c.157_187+178del Pathogenic ★ same condition
RDH12 c.344-43_421del Pathogenic ★ same condition
RDH12 p.Ala227fs Pathogenic ★ same condition
RDH12 p.Cys268fs Likely pathogenic ★ same condition
RDH12 p.Ile105fs Pathogenic ★ same condition
RDH12 p.Leu15_Tyr16insTer 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/rdh12-c-69del (accessed [today's date]).

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