NUBPL p.Ser97=
c.291G>A · rs766316675 · VCV1896840
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0153%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.28 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.34 | loss · gain 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 7.4 | GERP 6.1, phastCons 1 |
| Overall | ||
| CADD | 23.0 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0153%
Admixed American · 9/58,866 alleles
Filtering AF
0.00797%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00588%
Overall
0.00118%
18/1,527,556 alleles · ultra-rare
exomes 16/1,375,560 · genomes 2/151,996 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0153% | 6,541 |
| South Asian | 0.00245% | 40,878 |
| Remaining individualsnot grpmax-eligible | 0.00169% | 59,022 |
| African / African-American | 0.00136% | 73,462 |
| European (non-Finnish) | 0.000449% | 222,649 |
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.Ser97=
- Coding
- c.291G>A
- MANE Select
- NM_025152
- dbSNP
- rs766316675
- Type
- single nucleotide variant
- Location
- chr14:31565048 (GRCh38)
- Gene constraint
- LOEUF 0.896 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.40
Similar variants
- NUBPL p.Ser97Leu Uncertain significance ★★ ⚠ same residue
- 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
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-ser97 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown