PARD3 p.His86=
c.258C>T · rs112281243 · VCV714451
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 4.54%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.21 | GERP -4.5, phastCons 0.002 |
| Overall | ||
| CADD | 7.46 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
4.54%
African / African-American · 3,405/75,040 alleles
Filtering AF
4.41%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 4.36%
Overall
0.249%
4,020/1,614,132 alleles · low-frequency
exomes 2,059/1,461,826 · genomes 1,961/152,306 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 4.54% | 22 |
| Remaining individualsnot grpmax-eligible | 0.35% | 285 |
| Admixed American | 0.315% | 318 |
| Ashkenazi Jewishnot grpmax-eligible | 0.28% | 357 |
| Middle Eastern | 0.264% | 379 |
| European (non-Finnish) | 0.00847% | 11,800 |
| South Asian | 0.00659% | 15,180 |
| East Asian | 0.00446% | 22,435 |
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
- PARD3
- Protein
- p.His86=
- Coding
- c.258C>T
- MANE Select
- NM_001184785
- dbSNP
- rs112281243
- Type
- single nucleotide variant
- Location
- chr10:34517124 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37 · 1 PDB
- Residue 86
- the 'disordered' region
Similar variants
- PARD3 c.2560+10A>G Benign ★★ same type
- PARD3 p.Ala934Val Benign ★★ same type
- PARD3 p.Glu107Asp Benign ★★ same type
- PARD3 p.Glu1252= Benign/Likely benign ★★ same type
- PARD3 p.Ser798Asn Benign ★★ same type
- ASIP p.Ser72Pro Uncertain significance ★ ⚠ same type
- PARD3 p.Ala1062Thr Uncertain significance ★ ⚠ same type
- PARD3 p.Ala1337Pro 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/pard3-p-his86 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown