CLRN1 p.Cys20Ter
c.60T>A · rs1168480900 · VCV2839908
Pathogenic
Single submitter
Classification
Pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 1 of 3 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.26 | GERP -2.2, phastCons 0.001 |
| Overall | ||
| CADD | 29.6 | 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.Cys20Ter
- Coding
- c.60T>A
- MANE Select
- NM_174878
- dbSNP
- rs1168480900
- Type
- single nucleotide variant
- Location
- chr3:150972649 (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.Cys20Arg Uncertain significance ★ ⚠ same residue
- CLRN1 p.Cys20Ser Uncertain significance ★ ⚠ same residue
- CLRN1 p.Cys20= Likely benign ★ 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
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-cys20ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown