NBAS p.Pro297=
c.891G>A · rs143803321 · VCV737589
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.339%, afr)
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 -1.8 | GERP -3.4 |
| Overall | ||
| CADD | 5.249 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.339%
African / African-American · 254/74,930 alleles
Filtering AF
0.305%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.291%
Overall
0.0176%
284/1,610,868 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.339% | 295 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,201 |
| Admixed American | 0.015% | 6,665 |
| East Asian | 0.00446% | 22,406 |
| South Asian | 0.0022% | 45,504 |
| European (non-Finnish) | 0.000425% | 235,448 |
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
- NBAS
- Protein
- p.Pro297=
- Coding
- c.891G>A
- MANE Select
- NM_015909
- dbSNP
- rs143803321
- Type
- single nucleotide variant
- Location
- chr2:15504208 (GRCh38)
- Gene constraint
- LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.42
- Residue 297
- a UniProt-annotated variant site (in ilfs2; uncertain significance); the 'interaction with use1' region
Similar variants
- NBAS p.Pro297Arg Uncertain significance ★ ⚠ same residue
- NBAS p.Pro297Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
- NBAS c.1726-2A>G Likely pathogenic ★★ same type
- NBAS c.173-2A>G Likely pathogenic ★★ same type
- NBAS c.209+2T>G Pathogenic/Likely pathogenic ★★ same type
- NBAS c.2423+404G>C Likely pathogenic ★★ same type
- NBAS c.335+1G>C Pathogenic/Likely pathogenic ★★ same type
- NBAS c.4461+2T>C 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/nbas-p-pro297 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown