CLTC p.Asp471=
c.1413C>T · rs373501671 · VCV1560127
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0908%, 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 -1.1 | GERP -2.8, phastCons 0.001 |
| Overall | ||
| CADD | 8.942 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0908%
African / African-American · 68/74,866 alleles
Filtering AF
0.0734%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0672%
Overall
0.00496%
80/1,613,546 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0908% | 1,101 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,412 |
| Admixed American | 0.00334% | 29,967 |
| European (non-Finnish) | 0.000339% | 294,945 |
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
- CLTC
- Protein
- p.Asp471=
- Coding
- c.1413C>T
- MANE Select
- NM_004859
- dbSNP
- rs373501671
- Type
- single nucleotide variant
- Location
- chr17:59663886 (GRCh38)
- Gene constraint
- LOEUF 0.104 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 75.62 · 10 PDB
- Residue 471
- the 'involved in spindle localization and interaction with tacc3' region; the 'globular terminal domain' region
Similar variants
- CLTC p.Asp471Glu 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
- CLTC p.Tyr803Ter 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-asp471 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown