PARD3 p.Glu946=
c.2838A>G · rs148970712 · VCV3041037
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.132%, afr)
Conditions
1
PARD3-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.53 | acceptor loss · deltas |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.4 | GERP 1, phastCons 1 |
| Overall | ||
| CADD | 15.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.132%
African / African-American · 97/73,574 alleles
Filtering AF
0.111%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.103%
Overall
0.00672%
107/1,592,708 alleles · rare
exomes 50/1,440,576 · genomes 57/152,132 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.132% | 758 |
| Admixed American | 0.0126% | 7,931 |
| Remaining individualsnot grpmax-eligible | 0.00325% | 30,794 |
| European (non-Finnish) | 8.53e-05% | 1,172,844 |
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.Glu946=
- Coding
- c.2838A>G
- MANE Select
- NM_001184785
- dbSNP
- rs148970712
- Type
- single nucleotide variant
- Location
- chr10:34317334 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37 · 1 PDB
- Residue 946
- the 'interaction with frmd4a' region; the 'disordered' region
Disease context
PARD3-related disorder
Similar variants
- PARD3 c.2068-7T>C Likely benign same condition
- PARD3 c.3419+8C>T Likely benign same condition
- PARD3 c.715-4C>T Likely benign same condition
- PARD3 c.*4C>T Benign same condition
- PARD3 p.Ala93= Likely benign same condition
- PARD3 p.Arg1191= Benign same condition
- PARD3 p.Arg987= Likely benign same condition
- PARD3 p.Asn452Asp Likely benign same condition
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-glu946 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown