PIGK p.Pro78=
c.234T>C · rs148725038 · VCV3067359
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.119%, sas)
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 3.8 | GERP 0.53, phastCons 1 |
| Overall | ||
| CADD | 11.47 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.119%
South Asian · 107/90,084 alleles
Filtering AF
0.101%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0937%
Overall
0.00811%
128/1,578,704 alleles · rare
exomes 124/1,426,394 · genomes 4/152,310 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.119% | 842 |
| Middle Eastern | 0.0836% | 1,196 |
| Remaining individualsnot grpmax-eligible | 0.00815% | 12,264 |
| European (non-Finnish) | 0.000958% | 104,392 |
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
- PIGK
- Protein
- p.Pro78=
- Coding
- c.234T>C
- MANE Select
- NM_005482
- dbSNP
- rs148725038
- Type
- single nucleotide variant
- Location
- chr1:77206645 (GRCh38)
- Gene constraint
- LOEUF 1.915 · pLI 0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 85.08 · 4 PDB
- Residue 78
- a UniProt-annotated variant site (in nedhcas)
Similar variants
- PIGK c.-2A>T Uncertain significance ★★ same type
- PIGK p.Arg133Trp Uncertain significance ★★ ⚠ same type
- PIGK p.Thr313Lys Uncertain significance ★★ ⚠ same type
- PIGK c.703-6C>T Benign ★★ same type
- PIGK c.*2C>G Benign ★★ same type
- PIGK p.Thr16Ala Benign ★★ same type
- PIGK p.Tyr124= Benign ★★ same type
- PIGK p.Arg54Ter 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/pigk-p-pro78 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown