UBAP1 p.Ile72=
c.216C>T · VCV4902989
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0208%, amr)
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 0.016 | GERP 0.014, phastCons 0.79 |
| Overall | ||
| CADD | 9.701 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0208%
Admixed American · 9/43,222 alleles
Filtering AF
0.0109%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00805%
Overall
0.00494%
74/1,499,098 alleles · ultra-rare
exomes 66/1,346,986 · genomes 8/152,112 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0208% | 4,802 |
| Remaining individualsnot grpmax-eligible | 0.00522% | 19,171 |
| European (non-Finnish) | 0.00507% | 19,738 |
| South Asian | 0.00291% | 34,307 |
| African / African-American | 0.0028% | 35,713 |
| Finnishnot grpmax-eligible | 0.00167% | 59,894 |
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
- UBAP1
- Protein
- p.Ile72=
- Coding
- c.216C>T
- MANE Select
- NM_016525
- Type
- single nucleotide variant
- Location
- chr9:34241241 (GRCh38)
- Gene constraint
- LOEUF 0.285 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.60 · 3 PDB
- Residue 72
- the 'interaction with escrt-i' region
Similar variants
- UBAP1 p.Glu445Lys Uncertain significance ★★ ⚠ same type
- UBAP1 c.1083+136G>A Benign ★★ same type
- UBAP1 c.1083+86C>T Benign ★★ same type
- UBAP1 c.1266+6C>T Benign/Likely benign ★★ same type
- UBAP1 c.-7-51G>A Benign ★★ same type
- UBAP1 p.Asn198Ser Benign/Likely benign ★★ same type
- UBAP1 p.Asn357Lys Benign ★★ same type
- UBAP1 c.-20C>T 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/ubap1-p-ile72 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown