CLUAP1 p.Ala144=
c.432G>A · rs564836103 · VCV1630122
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.293%, sas)
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 -0.18 | GERP -2.4, phastCons 0.64 |
| Overall | ||
| CADD | 11.23 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.293%
South Asian · 267/91,082 alleles
Filtering AF
0.264%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.253%
Overall
0.0186%
300/1,614,014 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.293% | 341 |
| Remaining individualsnot grpmax-eligible | 0.024% | 4,166 |
| East Asian | 0.00892% | 11,216 |
| Admixed American | 0.00167% | 60,014 |
| European (non-Finnish) | 0.0011% | 90,764 |
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.Ala144=
- Coding
- c.432G>A
- MANE Select
- NM_015041
- dbSNP
- rs564836103
- Type
- single nucleotide variant
- Location
- chr16:3512415 (GRCh38)
- Gene constraint
- LOEUF 1.23 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.02
Similar variants
- CLUAP1 p.Ala144Pro Uncertain significance ★ ⚠ same residue
- 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
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-ala144 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown