MPIG6B p.Ser89=
c.267T>C · VCV4974137
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.221%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · T>A here scores Δ0.62 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -2.7 | GERP -3.2 |
| Overall | ||
| CADD | 2.171 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.221%
African / African-American · 165/74,806 alleles
Filtering AF
0.193%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.183%
Overall
0.0114%
183/1,610,780 alleles · rare
exomes 82/1,458,506 · genomes 101/152,274 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.221% | 453 |
| Admixed American | 0.0135% | 7,381 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,344 |
| South Asian | 0.0011% | 90,662 |
| European (non-Finnish) | 0.000679% | 147,354 |
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
- MPIG6B
- Protein
- p.Ser89=
- Coding
- c.267T>C
- MANE Select
- NM_138272
- Type
- single nucleotide variant
- Location
- chr6:31723844 (GRCh38)
- Gene constraint
- LOEUF 1.276 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.01 · 1 PDB
Similar variants
- MPIG6B p.Arg175Ter Pathogenic/Likely pathogenic ★★ same type
- MPIG6B p.Cys108Ter Pathogenic ★★ same type
- MPIG6B p.Thr186= Likely pathogenic ★★ same type
- MPIG6B c.542-9C>G Uncertain significance ★★ same type
- MPIG6B p.Ala21Gly Uncertain significance ★★ ⚠ same type
- MPIG6B p.Ala52Thr Uncertain significance ★★ ⚠ same type
- MPIG6B p.Arg83His Uncertain significance ★★ ⚠ same type
- MPIG6B p.Arg175Gly Benign/Likely benign ★★ 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/mpig6b-p-ser89 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown