Is BGN p.Asp319Tyr (c.955G>T) pathogenic?

BGN p.Asp319Tyr (c.955G>T) is classified Uncertain significance in BGN (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-21). AlphaMissense: likely pathogenic (0.976); No allele count reported in gnomAD v4.1 (AN 1,212,115).

How common is BGN p.Asp319Tyr (c.955G>T) in the general population?

BGN p.Asp319Tyr (c.955G>T) is no allele count reported in gnomAD v4.1 (AN 1,212,115) (gnomAD).

What do computational predictors say about BGN p.Asp319Tyr (c.955G>T)?

AlphaMissense predicts likely pathogenic (score 0.976) — an in-silico prediction, not a clinical call.

BGN p.Asp319Tyr

c.955G>T · VCV3766472

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely pathogenic

0.976 · ACMG-weighted

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,212,115)

Missense predictors

2/2 damaging

AlphaMissense, SaProt · REVEL indeterminate

Computational evidence

Protein change
AlphaMissense	0.976	likely pathogenic
REVEL	0.624	indeterminate
SaProt	LLR -14.07	damaging
⇒ AlphaMissense and SaProt both call this damaging; REVEL is indeterminate.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 9.8	GERP 2, phastCons 1
Regional constraint	o/e 0.94	unconstrained · MANE · 3,810 bp · p 0.25 · regional, not allelic
Overall
CADD	26.4	PHRED · no single calibrated threshold — expert panels disagree

ClinVar classifies this uncertain; the computational predictors unanimously lean damaging — a triage signal, not a reclassification

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,212,115). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: BGN
Protein: p.Asp319Tyr
Coding: c.955G>T
MANE Select: NM_001711
Type: single nucleotide variant
Location: chrX:153508293 (GRCh38)
Structure: AlphaFold pLDDT 85.72

Full BGN gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Similar variants

BGN p.Asp319Ala Uncertain significance ★ ⚠ same residue
BGN p.Asp319Asn Uncertain significance ★ ⚠ same residue
BGN c.770+1G>A Likely pathogenic ★★ same type
BGN p.Gln75Ter Pathogenic/Likely pathogenic ★★ same type
BGN p.Trp25Ter Likely pathogenic ★★ same type
BGN c.909+4A>G Uncertain significance ★★ same type
BGN p.Ala330Asp Uncertain significance ★★ ⚠ same type
BGN p.Ala330Pro Uncertain significance ★★ ⚠ 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/bgn-p-asp319tyr (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown