Is CERKL p.Phe456= (c.1368C>T) pathogenic?

CERKL p.Phe456= (c.1368C>T) is classified Likely benign in CERKL (ClinVar, Single submitter, 2 submitters; last evaluated 2022-09-06). Very rare (popmax 6.36e-05%); Associated with retinitis pigmentosa 26.

What condition is associated with CERKL p.Phe456= (c.1368C>T)?

CERKL p.Phe456= (c.1368C>T) is associated with retinitis pigmentosa 26 (ClinVar).

How common is CERKL p.Phe456= (c.1368C>T) in the general population?

CERKL p.Phe456= (c.1368C>T) is very rare (popmax 6.36e-05%) (gnomAD).

How is Retinitis pigmentosa inherited?

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

CERKL p.Phe456=

c.1368C>T · rs1687372607 · VCV991254

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 6.36e-05%)

Conditions

retinitis pigmentosa 26

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 1.8	GERP -1.9, phastCons 1
Overall
CADD	7.058	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 6.36e-05%

Overall 6.36e-05% 1/1,573,050 alleles · very rare exomes 1/1,420,864 · genomes 0/152,186 · 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: CERKL
Protein: p.Phe456=
Coding: c.1368C>T
MANE Select: NM_201548
dbSNP: rs1687372607
Type: single nucleotide variant
Location: chr2:181539262 (GRCh38)
Gene constraint: LOEUF 1.43 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 79.82

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

Disease context

retinitis pigmentosa 26 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Retinitis pigmentosa (Orphanet):

Inheritance: Autosomal dominant, Autosomal recessive, Mitochondrial inheritance
Onset: Adolescent, Adult, Childhood
Prevalence: 1-5 / 10 000 (Europe)

Similar variants

CERKL c.1074-1G>C Pathogenic/Likely pathogenic ★★ same condition
CERKL c.1074-2A>C Likely pathogenic ★★ same condition
CERKL c.1074-2A>G Likely pathogenic ★★ same condition
CERKL c.1365+1G>A Likely pathogenic ★★ same condition
CERKL c.1366-1G>A Likely pathogenic ★★ same condition
CERKL c.1366-1G>T Likely pathogenic ★★ same condition
CERKL c.1366-2A>G Likely pathogenic ★★ same condition
CERKL c.238+1G>A 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/cerkl-p-phe456 (accessed [today's date]).

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