Is CLRN1 p.Phe124fs (c.372del) pathogenic?

CLRN1 p.Phe124fs (c.372del) is classified Likely pathogenic in CLRN1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2018-03-02). No gnomAD frequency available for this variant; Associated with Usher syndrome type 3A.

What condition is associated with CLRN1 p.Phe124fs (c.372del)?

CLRN1 p.Phe124fs (c.372del) is associated with Usher syndrome type 3A (ClinVar).

How common is CLRN1 p.Phe124fs (c.372del) in the general population?

CLRN1 p.Phe124fs (c.372del) is no gnomAD frequency available for this variant (gnomAD).

CLRN1 p.Phe124fs

c.372del · rs1553772595 · VCV557009

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Usher syndrome type 3A

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 2 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 7.7	GERP 1.4, phastCons 1

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.Phe124fs
Coding: c.372del
MANE Select: NM_174878
dbSNP: rs1553772595
Type: Deletion
Location: chr3:150941643 (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

Usher syndrome type 3A — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

CLRN1 p.Phe193fs Pathogenic/Likely pathogenic ★★ same condition
CLRN1 p.Val101fs Pathogenic ★★ same condition
CLRN1 p.Leu32fs Pathogenic ★ same condition
CLRN1 p.Leu76fs Pathogenic ★ same condition
CLRN1 p.Phe128fs Likely pathogenic ★ same condition
CLRN1 c.-10_253+10del Pathogenic same condition
CLRN1 p.Val114fs Likely pathogenic same condition
CLRN1 c.254-2099_254-2086del Uncertain significance 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-phe124fs (accessed [today's date]).

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