NBAS p.Phe1791Ser
c.5372T>C · VCV3257321
Computational evidence
| Protein change | ||
| AlphaMissense | 0.8455 | likely pathogenic · top 9% in NBAS |
|---|---|---|
| REVEL | 0.267 | benign-leaning |
| SaProt | LLR -10.23 | damaging |
| ⇒ AlphaMissense and SaProt call this damaging; REVEL does not. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 11 | GERP 2.6, phastCons 1 |
| Regional constraint | o/e 1.03 | unconstrained · MANE · 394 kb · p 0.09 · regional, not allelic |
| Overall | ||
| CADD | 24.3 | PHRED · no single calibrated threshold — expert panels disagree |
AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.
Population frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00133% | 75,028 |
| European (non-Finnish) | 8.47e-05% | 1,179,948 |
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.Phe1791Ser
- Coding
- c.5372T>C
- MANE Select
- NM_015909
- Type
- single nucleotide variant
- Location
- chr2:15276868 (GRCh38)
- Gene constraint
- LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.42
- Residue 1791
- 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); a UniProt-annotated variant site (found in a patient with a multisystem disease involving liver, eye, immune system, connective tissue and bone; uncertain significance; reduced protein expression levels in fibroblasts); a UniProt-annotated variant site (found in a patient with a multisystem disease involving liver, eye, immune system, connective tissue and bone; uncertain significance; reduced collagen secretion; diffuse collagen bundles; reduced protein expression in fibroblasts); the 'interaction with zw10 and rint1' 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-phe1791ser (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown