Is RDH12 p.Phe152= (c.456C>T) pathogenic?

RDH12 p.Phe152= (c.456C>T) is classified Likely benign in RDH12 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-11). Very rare (popmax 0.00801%, afr); Associated with Leber congenital amaurosis 13.

What condition is associated with RDH12 p.Phe152= (c.456C>T)?

RDH12 p.Phe152= (c.456C>T) is associated with Leber congenital amaurosis 13 (ClinVar).

How common is RDH12 p.Phe152= (c.456C>T) in the general population?

RDH12 p.Phe152= (c.456C>T) is very rare (popmax 0.00801%, afr) (gnomAD).

How is Leber congenital amaurosis inherited?

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

RDH12 p.Phe152=

c.456C>T · rs1191351202 · VCV1147676

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00801%, afr)

Conditions

Leber congenital amaurosis 13

⚠ Built without this gene's context — gene constraint and dosage, protein structure, pathways, panels and related-variant links were not looked up for this page. why

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not looked up on this page · why
Constraint at this position
Conservation	phyloP 0.15	GERP -1.8, phastCons 0.96
Overall
CADD	6.929	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00801% African / African-American · 6/74,878 alleles

Filtering AF 0.00347% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00229%

Overall 0.000372% 6/1,612,444 alleles · very rare exomes 4/1,460,236 · genomes 2/152,208 · joint denominator

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: RDH12
Protein: p.Phe152=
Coding: c.456C>T
MANE Select: NM_152443
dbSNP: rs1191351202
Type: single nucleotide variant
Location: chr14:67726988 (GRCh38)

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)

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-p-phe152 (accessed [today's date]).

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