CLRN1 p.Leu39=
c.117C>T · rs748584811 · VCV1154387
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.015%, amr)
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 3.4 | GERP -0.23, phastCons 1 |
| Overall | ||
| CADD | 9.671 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.015%
Admixed American · 9/60,014 alleles
Filtering AF
0.00773%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00578%
Overall
0.00062%
10/1,614,126 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.015% | 6,668 |
| European (non-Finnish) | 8.47e-05% | 1,180,050 |
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.Leu39=
- Coding
- c.117C>T
- MANE Select
- NM_174878
- dbSNP
- rs748584811
- Type
- single nucleotide variant
- Location
- chr3:150972592 (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 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
- CLRN1 p.Ala123Asp Pathogenic/Likely pathogenic ★★ same type
- CLRN1 p.Arg207Ter Pathogenic/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-leu39 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown