CLTC p.Arg523=
c.1569A>T · rs912653558 · VCV1661961
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
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. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.2 | GERP -3.2 |
| Overall | ||
| CADD | 4.471 | PHRED · no single calibrated threshold — expert panels disagree |
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
- CLTC
- Protein
- p.Arg523=
- Coding
- c.1569A>T
- MANE Select
- NM_004859
- dbSNP
- rs912653558
- Type
- single nucleotide variant
- Location
- chr17:59664834 (GRCh38)
- Gene constraint
- LOEUF 0.104 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.62 · 10 PDB
- Residue 523
- the 'flexible linker' region
Similar variants
- CLTC p.Arg523Gln Uncertain significance ★★ ⚠ same residue
- CLTC p.Arg523Pro Uncertain significance ★ ⚠ same residue
- CLTC p.Arg1165Ter Likely pathogenic ★★ same type
- CLTC p.Arg1251Ter Pathogenic/Likely pathogenic ★★ same type
- CLTC p.Arg1311Ter Likely pathogenic ★★ same type
- CLTC p.Arg63Ter Pathogenic ★★ same type
- CLTC p.Pro890Leu Pathogenic/Likely pathogenic ★★ same type
- CLTC p.Tyr1574Ter 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/cltc-p-arg523 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown