NBAS p.Val1682Ile
c.5044G>A · rs371029230 · VCV1440696
Computational evidence
| Protein change | ||
| AlphaMissense | 0.0966 | likely benign |
|---|---|---|
| REVEL | 0.16 | moderately benign-leaning |
| SaProt | LLR -6.90 | tolerated |
| ⇒ AlphaMissense, REVEL and SaProt all call this tolerated. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 4.8 | GERP 1.7, phastCons 1 |
| Regional constraint | o/e 1.03 | unconstrained · MANE · 394 kb · p 0.09 · regional, not allelic |
| Overall | ||
| CADD | 23.1 | 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 |
|---|---|---|
| Middle Easterngrpmax | 0.0164% | 6,082 |
| African / African-American | 0.012% | 8,323 |
| Admixed American | 0.00667% | 14,999 |
| South Asian | 0.00549% | 18,216 |
| European (non-Finnish) | 0.00492% | 20,341 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,452 |
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.Val1682Ile
- Coding
- c.5044G>A
- MANE Select
- NM_015909
- dbSNP
- rs371029230
- Type
- single nucleotide variant
- Location
- chr2:15287167 (GRCh38)
- Gene constraint
- LOEUF 0.761 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 74.42
- Residue 1682
- 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 p.Val1682Phe Uncertain significance ★ ⚠ same residue
- NBAS p.Ala1568Val Uncertain significance ★★ ⚠ same condition
- NBAS p.Ala1645Val Uncertain significance ★★ ⚠ same condition
- NBAS p.Ala1795Val Uncertain significance ★★ ⚠ same condition
- NBAS p.Ala1941Gly Uncertain significance ★★ ⚠ same condition
- NBAS p.Ala195Thr Uncertain significance ★★ ⚠ same condition
- NBAS p.Ala2005Thr Uncertain significance ★★ ⚠ same condition
- NBAS p.Ala2341Val Uncertain significance ★★ ⚠ same condition
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-val1682ile (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown