PARD3 p.Ser1233=
c.3699C>T · rs374281684 · VCV3052539
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00359%, nfe)
Conditions
1
PARD3-related disorder
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 1.2 | GERP -3.3, phastCons 1 |
| Overall | ||
| CADD | 4.443 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00359%
European (non-Finnish) · 42/1,170,648 alleles
Filtering AF
0.00269%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00238%
Overall
0.00269%
43/1,600,688 alleles · very rare
exomes 40/1,448,568 · genomes 3/152,120 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00359% | 27,873 |
| African / African-American | 0.00134% | 74,494 |
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.Ser1233=
- Coding
- c.3699C>T
- MANE Select
- NM_001184785
- dbSNP
- rs374281684
- Type
- single nucleotide variant
- Location
- chr10:34111532 (GRCh38)
- Gene constraint
- LOEUF 0.61 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.37 · 1 PDB
- Residue 1233
- 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-ser1233 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown