BEX4 p.Gln98=
c.294G>A · rs144455353 · VCV2661091
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00704%, nfe)
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 -0.67 | GERP -2.5 |
| Overall | ||
| CADD | 5.596 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00704%
European (non-Finnish) · 63/894,904 alleles
Filtering AF
0.00562%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00511%
Overall
0.00562%
68/1,209,820 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00704% | 14,205 |
| Remaining individualsnot grpmax-eligible | 0.0063% | 15,864 |
| Admixed American | 0.00218% | 45,841 |
| African / African-American | 0.00175% | 57,195 |
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
- BEX4
- Protein
- p.Gln98=
- Coding
- c.294G>A
- MANE Select
- NM_001080425
- dbSNP
- rs144455353
- Type
- single nucleotide variant
- Location
- chrX:103216447 (GRCh38)
- Structure
- AlphaFold pLDDT 64.35
- Residue 98
- the 'interaction with alpha-tubulin' region
Similar variants
- BEX4 p.Ala65Val Uncertain significance ★ ⚠ same type
- BEX4 p.Arg104His Uncertain significance ★ ⚠ same type
- BEX4 p.Arg104Ser Uncertain significance ★ ⚠ same type
- BEX4 p.Arg52Trp Uncertain significance ★ ⚠ same type
- BEX4 p.Arg54Gln Uncertain significance ★ ⚠ same type
- BEX4 p.Arg63Gln Uncertain significance ★ ⚠ same type
- BEX4 p.Asn112His Uncertain significance ★ ⚠ same type
- BEX4 p.Asn11Ser 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/bex4-p-gln98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown