CLP1 p.Leu415=
c.1245C>T · rs113696908 · VCV1980198
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.04%, afr)
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 0.25 | GERP -0.4, phastCons 0.94 |
| Overall | ||
| CADD | 7.066 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.04%
African / African-American · 30/75,030 alleles
Filtering AF
0.0288%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0249%
Overall
0.00316%
51/1,613,282 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.04% | 2,501 |
| Remaining individualsnot grpmax-eligible | 0.0304% | 3,287 |
| Admixed American | 0.00167% | 59,956 |
| European (non-Finnish) | 8.48e-05% | 1,179,568 |
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
- CLP1
- Protein
- p.Leu415=
- Coding
- c.1245C>T
- MANE Select
- NM_006831
- dbSNP
- rs113696908
- Type
- single nucleotide variant
- Location
- chr11:57661403 (GRCh38)
- Gene constraint
- LOEUF 0.856 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 93.95 · 2 PDB
- Residue 415
- a β-strand
Similar variants
- CLP1 p.Arg140His Pathogenic/Likely pathogenic ★★ same type
- CLP1 p.Arg116Gln Uncertain significance ★★ ⚠ same type
- CLP1 p.Arg143Cys Uncertain significance ★★ ⚠ same type
- CLP1 p.Arg288Cys Uncertain significance ★★ ⚠ same type
- CLP1 p.Arg288His Uncertain significance ★★ ⚠ same type
- CLP1 p.Asn95Ser Uncertain significance ★★ ⚠ same type
- CLP1 p.Cys215Tyr Uncertain significance ★★ ⚠ same type
- CLP1 p.Glu175Lys 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/clp1-p-leu415 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown