UBAP2L p.Ser596=
c.1788C>T · VCV3905225
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.28%, 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 0.61 | phastCons 0.98 |
| Overall | ||
| CADD | 10.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.28%
South Asian · 1,116/87,268 alleles
Filtering AF
1.22%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.19%
Overall
0.0741%
1,175/1,586,760 alleles · low-frequency
exomes 1,118/1,440,574 · genomes 57/146,186 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 1.28% | 78 |
| Remaining individualsnot grpmax-eligible | 0.0522% | 1,915 |
| Middle Eastern | 0.0335% | 2,983 |
| African / African-American | 0.00693% | 14,426 |
| Admixed American | 0.0069% | 14,484 |
| Finnishnot grpmax-eligible | 0.00476% | 21,029 |
| East Asian | 0.00231% | 43,330 |
| European (non-Finnish) | 0.00103% | 97,169 |
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
- UBAP2L
- Protein
- p.Ser596=
- Coding
- c.1788C>T
- MANE Select
- NM_014847
- Type
- single nucleotide variant
- Location
- chr1:154254023 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 42.99
- Residue 596
- a UniProt-annotated variant site (in nedlbf; pathogenic; decreased protein expression in patients cells; patient cells contain a novel protein which lacks the normal n-terminus and is produced by translation from a start codon downstream the nonsense variant; decreased function in stress granule formation shown by rescue assays in transfected ubap2l-deficient cells); a UniProt-annotated variant site (in nedlbf; pathogenic); a UniProt-annotated variant site (in nedlbf; pathogenic; decreased function in stress granule formation shown by rescue assays in transfected ubap2l-deficient cells); the 'disordered' region
Similar variants
- UBAP2L p.Ser596Cys Uncertain significance ★ ⚠ same residue
- UBAP2L p.Arg187Ter Pathogenic/Likely pathogenic ★★ same type
- UBAP2L p.Arg421His Uncertain significance ★★ ⚠ same type
- UBAP2L p.Pro1072Ser Uncertain significance ★★ ⚠ same type
- UBAP2L p.Pro957Leu Uncertain significance ★★ ⚠ same type
- UBAP2L p.Val528Ile Uncertain significance ★★ ⚠ same type
- UBAP2L p.Ser950= Benign ★★ same type
- UBAP2L c.3168+3A>G 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/ubap2l-p-ser596 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown