CLRN1 p.Val47=
c.141C>G · rs2107997038 · VCV1102564
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
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 3.1 | GERP -1.2, phastCons 1 |
| Overall | ||
| CADD | 7.198 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,892 alleles
Overall
6.84e-05%
1/1,461,888 alleles · very rare
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
- CLRN1
- Protein
- p.Val47=
- Coding
- c.141C>G
- MANE Select
- NM_174878
- dbSNP
- rs2107997038
- Type
- single nucleotide variant
- Location
- chr3:150972568 (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.Val47Ile Uncertain significance ★★ ⚠ same residue
- CLRN1 p.Val47fs Pathogenic/Likely pathogenic ★★ same residue
- CLRN1 c.253+1G>A Likely pathogenic ★★ same type
- CLRN1 c.253+6T>C Pathogenic/Likely pathogenic ★★ same type
- CLRN1 c.254-2A>G Pathogenic/Likely pathogenic ★★ same type
- CLRN1 c.254-649T>G Pathogenic/Likely pathogenic ★★ same type
- CLRN1 c.433+1G>A Pathogenic/Likely pathogenic ★★ same type
- CLRN1 c.433+1G>T Likely pathogenic ★★ same type
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-val47 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown