Is CLRN1 p.Ala19fs (c.55del) pathogenic?

CLRN1 p.Ala19fs (c.55del) is classified Likely pathogenic in CLRN1 (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-28). Absent from gnomAD; Associated with retinitis pigmentosa 61.

What condition is associated with CLRN1 p.Ala19fs (c.55del)?

CLRN1 p.Ala19fs (c.55del) is associated with retinitis pigmentosa 61 (ClinVar).

How common is CLRN1 p.Ala19fs (c.55del) in the general population?

CLRN1 p.Ala19fs (c.55del) is absent from gnomAD (gnomAD).

How is Retinitis pigmentosa inherited?

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

CLRN1 p.Ala19fs

c.55del · rs2472831512 · VCV3241181

Likely pathogenic Single submitter

Classification

Likely 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

retinitis pigmentosa 61

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 1 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.6	GERP -3.4

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: CLRN1
Protein: p.Ala19fs
Coding: c.55del
MANE Select: NM_174878
dbSNP: rs2472831512
Type: Deletion
Location: chr3:150972654 (GRCh38)
Gene constraint: LOEUF 1.168 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 90.74

Full CLRN1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

retinitis pigmentosa 61 — 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

CLRN1 p.Phe193fs Pathogenic/Likely pathogenic ★★ same condition
CLRN1 p.Phe197fs Pathogenic ★★ same condition
CLRN1 p.Val101fs Pathogenic ★★ same condition
CLRN1 p.Val47fs Pathogenic/Likely pathogenic ★★ same condition
CLRN1 p.Ala19= Benign/Likely benign ★★ same residue
CLRN1 p.Ala44fs Likely pathogenic ★ same condition
CLRN1 p.Gly51fs Likely pathogenic ★ same condition
CLRN1 p.Ile153_Leu154delinsMet 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/clrn1-p-ala19fs (accessed [today's date]).

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