CLUAP1 p.Thr75=
c.225C>G · rs1446704250 · VCV1653911
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00411%, 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 -4.2, phastCons 0.046 |
| Overall | ||
| CADD | 5.062 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00411%
African / African-American · 3/73,024 alleles
Filtering AF
0.00109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000502%
Overall
0.000251%
4/1,591,172 alleles · very rare
exomes 1/1,439,620 · genomes 3/151,552 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00411% | 24,341 |
| East Asian | 0.00227% | 44,068 |
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
- CLUAP1
- Protein
- p.Thr75=
- Coding
- c.225C>G
- MANE Select
- NM_015041
- dbSNP
- rs1446704250
- Type
- single nucleotide variant
- Location
- chr16:3508294 (GRCh38)
- Gene constraint
- LOEUF 1.23 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.02
Similar variants
- CLUAP1 p.Ala152Glu Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Ala188Gly Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Ala339Thr Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Arg20Gln Uncertain significance ★★ same type
- CLUAP1 p.Arg228Gln Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Arg304His Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Arg332Gln Uncertain significance ★★ ⚠ same type
- CLUAP1 p.Asn296Lys 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/cluap1-p-thr75 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown