ITGB4 p.Ser1069=
c.3207C>T · rs2061298758 · VCV2779220
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00134%, afr)
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 -1.8 | |
| Overall | ||
| CADD | 4.332 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00134%
African / African-American · 1/74,904 alleles
Overall
6.2e-05%
1/1,613,176 alleles · very rare
exomes 0/1,461,052 · genomes 1/152,124 · joint denominator
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
- ITGB4
- Protein
- p.Ser1069=
- Coding
- c.3207C>T
- MANE Select
- NM_000213
- dbSNP
- rs2061298758
- Type
- single nucleotide variant
- Location
- chr17:75748936 (GRCh38)
- Gene constraint
- LOEUF 0.86 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 69.04 · 13 PDB
- Residue 1069
- the calx-beta domain; a modified residue (phosphoserine)
Similar variants
- ITGB4 p.Ser1069Pro Conflicting classifications of pathogenicity ★ ⚠ same residue
- ITGB4 c.1860+1G>A Likely pathogenic ★★ same type
- ITGB4 c.2254+1G>T Pathogenic/Likely pathogenic ★★ same type
- ITGB4 c.2550+1G>A Pathogenic/Likely pathogenic ★★ same type
- ITGB4 c.2633+1G>A Pathogenic/Likely pathogenic ★★ same type
- ITGB4 c.2783-2A>G Pathogenic/Likely pathogenic ★★ same type
- ITGB4 c.3793+1G>A Pathogenic ★★ same type
- ITGB4 p.Ala620= 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/itgb4-p-ser1069 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown