CLCC1 p.Leu13=
c.37C>T · rs780313648 · VCV1583393
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00221%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.24 | acceptor loss · deltas |
|---|---|---|
| Pangolin | Δ0.24 | loss · gain 0.19 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 3.2 | GERP 1.6, phastCons 1 |
| Overall | ||
| CADD | 6.384 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00221%
European (non-Finnish) · 26/1,177,930 alleles
Filtering AF
0.00154%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0013%
Overall
0.00161%
26/1,610,576 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
- CLCC1
- Protein
- p.Leu13=
- Coding
- c.37C>T
- MANE Select
- NM_001377458
- dbSNP
- rs780313648
- Type
- single nucleotide variant
- Location
- chr1:108950401 (GRCh38)
- Gene constraint
- LOEUF 0.778 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 61.13
Similar variants
- CLCC1 p.Asp25Glu Pathogenic/Likely pathogenic ★★ same type
- CLCC1 p.Ala245Thr Uncertain significance ★★ ⚠ same type
- CLCC1 p.Ala522Thr Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg208His Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg377Trp Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg381Trp Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg401Gly Uncertain significance ★★ ⚠ same type
- CLCC1 p.Arg443Trp Uncertain significance ★★ ⚠ 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/clcc1-p-leu13 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown