PARD3 p.Val113=
c.339C>G · rs41276096 · VCV2640403
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.99%, mid)
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 -0.86 | GERP -4.5 |
| Overall | ||
| CADD | 0.181 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.99%
Middle Eastern · 60/6,062 alleles
Filtering AF
0.789%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.717%
Overall
0.151%
2,434/1,614,212 alleles · rare
exomes 2,225/1,461,844 · genomes 209/152,368 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.99% | 101 |
| Ashkenazi Jewishnot grpmax-eligible | 0.432% | 231 |
| Remaining individualsnot grpmax-eligible | 0.171% | 584 |
| European (non-Finnish) | 0.164% | 610 |
| Admixed American | 0.13% | 770 |
| South Asian | 0.0769% | 1,301 |
| African / African-American | 0.0586% | 1,706 |
| Finnishnot grpmax-eligible | 0.0172% | 5,822 |
| East Asian | 0.00223% | 44,880 |
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.Val113=
- Coding
- c.339C>G
- MANE Select
- NM_001184785
- dbSNP
- rs41276096
- Type
- single nucleotide variant
- Location
- chr10:34517043 (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-val113 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown