CLRN1 p.Met1Ile
c.3G>A · rs1553776132 · VCV552903
Likely pathogenic
No assertion criteria
Classification
Likely pathogenic
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
Consequence
start-loss
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Usher syndrome type 3A
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | start-loss | predicted loss-of-function |
|---|---|---|
| REVEL | 0.827 | moderately pathogenic-leaning |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 6 | GERP 1.7, phastCons 1 |
| Overall | ||
| CADD | 25.7 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- CLRN1
- Protein
- p.Met1Ile
- Coding
- c.3G>A
- MANE Select
- NM_174878
- dbSNP
- rs1553776132
- Type
- single nucleotide variant
- Location
- chr3:150972706 (GRCh38)
- Gene constraint
- LOEUF 1.168 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 90.74
Similar variants
- CLRN1 p.Met1Thr Conflicting classifications of pathogenicity ★ same residue
- CLRN1 c.253+1G>A Likely pathogenic ★★ same condition
- CLRN1 c.253+6T>C Pathogenic/Likely pathogenic ★★ same condition
- CLRN1 p.Ala123Asp Pathogenic/Likely pathogenic ★★ same condition
- CLRN1 p.Arg207Ter Pathogenic/Likely pathogenic ★★ same condition
- CLRN1 p.Asn202Lys Pathogenic/Likely pathogenic ★★ same condition
- CLRN1 p.Asn48Lys Pathogenic ★★ same condition
- CLRN1 p.Gln181Ter Pathogenic/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-met1ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown