Is CLRN1 p.Val114fs (c.341del) pathogenic?

CLRN1 p.Val114fs (c.341del) is classified Likely pathogenic in CLRN1 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2022-09-18). Associated with Usher syndrome type 3A.

What condition is associated with CLRN1 p.Val114fs (c.341del)?

CLRN1 p.Val114fs (c.341del) is associated with Usher syndrome type 3A (ClinVar).

CLRN1 p.Val114fs

c.341del · VCV3024084

Likely pathogenic No assertion criteria

Classification

Likely pathogenic

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

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 1.6	GERP 1.4, phastCons 1

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: CLRN1
Protein: p.Val114fs
Coding: c.341del
MANE Select: NM_174878
Type: Deletion
Location: chr3:150941674 (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 p.Val114Ala Uncertain significance ★ ⚠ same residue
CLRN1 c.-10_253+10del Pathogenic same condition
CLRN1 p.Phe124fs 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-val114fs (accessed [today's date]).

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