BGN p.Trp2Ter
c.5G>A · rs886037823 · VCV265794
Likely pathogenic
Single submitter
Classification
Likely pathogenic
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
Consequence
nonsense (stop-gain)
predicted LoF
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
Meester-Loeys syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Consequence | nonsense (stop-gain) | predicted loss-of-function |
|---|---|---|
| NMD | predicted | premature termination codon in exon 2 of 8 |
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.5 | GERP -2.9, phastCons 0.91 |
| Overall | ||
| CADD | 32.0 | PHRED · no single calibrated threshold — expert panels disagree |
Predicted loss-of-function is descriptive, not an applied PVS1 code.
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- BGN
- Protein
- p.Trp2Ter
- Coding
- c.5G>A
- MANE Select
- NM_001711
- dbSNP
- rs886037823
- Type
- single nucleotide variant
- Location
- chrX:153504636 (GRCh38)
- Structure
- AlphaFold pLDDT 85.72
Similar variants
- BGN p.Trp2Arg Uncertain significance ★ ⚠ same residue
- BGN c.770+1G>A Likely pathogenic ★★ same condition
- BGN p.Gln75Ter Pathogenic/Likely pathogenic ★★ same condition
- BGN p.Trp25Ter Likely pathogenic ★★ same condition
- BGN p.Arg214Cys Uncertain significance ★★ ⚠ same condition
- BGN p.Gly66Ser Uncertain significance ★★ ⚠ same condition
- BGN p.Met62Thr Uncertain significance ★★ ⚠ same condition
- BGN c.238+75A>G Benign ★★ 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/bgn-p-trp2ter (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown