NBAS p.Glu537=
c.1611A>G · rs35454315 · VCV1164819
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.99%, eas)
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 -0.033 | GERP 0.6, phastCons 0.91 |
| Overall | ||
| CADD | 6.955 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.99%
East Asian · 2,240/44,856 alleles
Filtering AF
4.82%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.75%
Overall
0.542%
8,747/1,613,854 alleles · low-frequency
exomes 6,715/1,461,552 · genomes 2,032/152,302 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 4.99% | 20 |
| African / African-American | 2.98% | 34 |
| Admixed American | 2.09% | 48 |
| South Asian | 1.53% | 66 |
| Middle Eastern | 1.25% | 80 |
| Remaining individualsnot grpmax-eligible | 0.965% | 104 |
| Finnishnot grpmax-eligible | 0.105% | 955 |
| European (non-Finnish) | 0.0746% | 1,341 |
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.Glu537=
- Coding
- c.1611A>G
- MANE Select
- NM_015909
- dbSNP
- rs35454315
- Type
- single nucleotide variant
- Location
- chr2:15473336 (GRCh38)
- Gene constraint
- LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.42
- Residue 537
- a UniProt-annotated variant site (in ilfs2; uncertain significance); a UniProt-annotated variant site (found in a patient with a multisystem disease involving liver, eye, immune system, connective tissue and bone; uncertain significance); the 'interaction with use1' region
Similar variants
- 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
- NBAS c.4583-2A>G Likely pathogenic ★★ same type
- NBAS c.513+2T>C Pathogenic/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-glu537 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown