Is PARD3 p.Ser417= (c.1251T>C) pathogenic?

PARD3 p.Ser417= (c.1251T>C) is classified Likely benign in PARD3 (ClinVar, No assertion criteria, 1 submitter; last evaluated 2019-08-16). Absent from gnomAD v4.1; Associated with PARD3-related disorder.

What condition is associated with PARD3 p.Ser417= (c.1251T>C)?

PARD3 p.Ser417= (c.1251T>C) is associated with PARD3-related disorder (ClinVar).

How common is PARD3 p.Ser417= (c.1251T>C) in the general population?

PARD3 p.Ser417= (c.1251T>C) is absent from gnomAD v4.1 (gnomAD).

PARD3 p.Ser417=

c.1251T>C · rs2495869503 · VCV3053131

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

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 -0.91	GERP -4.8
Overall
CADD	0.67	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: PARD3
Protein: p.Ser417=
Coding: c.1251T>C
MANE Select: NM_001184785
dbSNP: rs2495869503
Type: single nucleotide variant
Location: chr10:34382688 (GRCh38)
Gene constraint: LOEUF 0.61 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 54.37 · 1 PDB
Residue 417: the 'disordered' region

Full PARD3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

PARD3-related disorder

Similar variants

PARD3 p.Ser417Phe Conflicting classifications of pathogenicity ★ ⚠ same residue
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

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-ser417 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown