UBAP1 p.Glu352=
c.1056A>G · VCV4902994
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000341%, nfe)
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 2.1 | GERP -1.7, phastCons 1 |
| Overall | ||
| CADD | 4.388 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000341%
European (non-Finnish) · 4/1,173,450 alleles
Filtering AF
8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.4e-05%
Overall
0.000249%
4/1,606,142 alleles · very rare
exomes 4/1,453,854 · genomes 0/152,288 · joint denominator
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.Glu352=
- Coding
- c.1056A>G
- MANE Select
- NM_016525
- Type
- single nucleotide variant
- Location
- chr9:34242081 (GRCh38)
- Gene constraint
- LOEUF 0.285 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.60 · 3 PDB
- Residue 352
- a UniProt-annotated variant site (in spg80); a UniProt-annotated variant site (in spg80; uncertain significance)
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-glu352 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown