PARD3 p.Leu587=
c.1761G>C · rs61735564 · VCV727332
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.761%, 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 1.5 | GERP 0.4, phastCons 1 |
| Overall | ||
| CADD | 6.197 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.761%
African / African-American · 571/75,058 alleles
Filtering AF
0.709%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.689%
Overall
0.0426%
687/1,614,000 alleles · rare
exomes 337/1,461,688 · genomes 350/152,312 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.761% | 131 |
| Admixed American | 0.1% | 1,000 |
| Middle Eastern | 0.099% | 1,010 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| European (non-Finnish) | 0.00229% | 43,698 |
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.Leu587=
- Coding
- c.1761G>C
- MANE Select
- NM_001184785
- dbSNP
- rs61735564
- Type
- single nucleotide variant
- Location
- chr10:34360206 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37 · 1 PDB
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-leu587 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown