UBAP2L p.Ser950=
c.2850G>A · rs36114119 · VCV767704
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.98%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.683 | pathogenic-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.58 | phastCons 0.99 |
| Overall | ||
| CADD | 11.91 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.98%
African / African-American · 3,732/74,984 alleles
Filtering AF
4.84%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.79%
Overall
0.279%
4,509/1,614,042 alleles · low-frequency
exomes 2,365/1,461,890 · genomes 2,144/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.98% | 20 |
| Remaining individualsnot grpmax-eligible | 0.394% | 254 |
| Admixed American | 0.387% | 259 |
| Middle Eastern | 0.247% | 404 |
| European (non-Finnish) | 0.0232% | 4,307 |
| South Asian | 0.00988% | 10,120 |
| East Asian | 0.00223% | 44,882 |
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.Ser950=
- Coding
- c.2850G>A
- MANE Select
- NM_014847
- dbSNP
- rs36114119
- Type
- single nucleotide variant
- Location
- chr1:154261645 (GRCh38)
- Gene constraint
- LOEUF 0.159 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 42.99
- Residue 950
- 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)
Similar variants
- 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 c.3168+3A>G Pathogenic ★ same type
- UBAP2L p.Gln616Ter Pathogenic ★ same type
- UBAP2L p.Gln990Ter 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/ubap2l-p-ser950 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown