NUBPL p.Val79=
c.237C>G · rs1300865369 · VCV1666352
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.29 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.22 | loss · gain 0.19 · SpliceAI calls gain · independent |
| Constraint at this position | ||
| Conservation | phyloP 4.2 | GERP 4, phastCons 1 |
| Overall | ||
| CADD | 16.25 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,872 alleles
Overall
6.2e-05%
1/1,613,830 alleles · very rare
exomes 1/1,461,616 · genomes 0/152,214 · 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
- NUBPL
- Protein
- p.Val79=
- Coding
- c.237C>G
- MANE Select
- NM_025152
- dbSNP
- rs1300865369
- Type
- single nucleotide variant
- Location
- chr14:31562196 (GRCh38)
- Gene constraint
- LOEUF 0.896 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.40
- Residue 79
- a binding site
Similar variants
- NUBPL c.693+1G>A Pathogenic/Likely pathogenic ★★ same type
- NUBPL p.Gln176Ter Likely pathogenic ★★ same type
- NUBPL p.Leu104Pro Pathogenic/Likely pathogenic ★★ same type
- NUBPL c.382+3A>G Uncertain significance ★★ same type
- NUBPL c.*1151G>A Uncertain significance ★★ same type
- NUBPL c.*806A>G Uncertain significance ★★ same type
- NUBPL p.Ala100Thr Uncertain significance ★★ ⚠ same type
- NUBPL p.Ala204Val 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/nubpl-p-val79 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown