ITGA8 p.Ser2=
c.6G>T · rs1835528151 · VCV2775609
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000283%, 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 -0.23 | GERP -4.1, phastCons 0.02 |
| Overall | ||
| CADD | 3.464 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000283%
European (non-Finnish) · 3/1,058,568 alleles
Filtering AF
7.5e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.1e-05%
Overall
0.000222%
3/1,348,382 alleles · very rare
exomes 3/1,200,122 · genomes 0/148,260 · 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
- ITGA8
- Protein
- p.Ser2=
- Coding
- c.6G>T
- MANE Select
- NM_003638
- dbSNP
- rs1835528151
- Type
- single nucleotide variant
- Location
- chr10:15719766 (GRCh38)
- Gene constraint
- LOEUF 0.801 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.08
Similar variants
- ITGA8 p.Ser2Trp Uncertain significance ★ ⚠ same residue
- ITGA8 c.2982+2T>C Pathogenic/Likely pathogenic ★★ same type
- ITGA8 p.Arg938Ter Pathogenic ★★ same type
- ITGA8 p.Gln876Ter Likely pathogenic ★★ same type
- ITGA8 p.Ala552Thr Uncertain significance ★★ ⚠ same type
- ITGA8 p.Ala848Ser Uncertain significance ★★ ⚠ same type
- ITGA8 p.Arg588Gln Uncertain significance ★★ ⚠ same type
- ITGA8 p.Asn40Thr 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/itga8-p-ser2 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown