Is PARD3 p.Ala934Val (c.2801C>T) pathogenic?

PARD3 p.Ala934Val (c.2801C>T) is classified Benign in PARD3 (ClinVar, Multiple submitters, 3 submitters; last evaluated 2019-12-31). AlphaMissense: likely benign (0.067); Low-frequency (popmax 1.01%, mid).

How common is PARD3 p.Ala934Val (c.2801C>T) in the general population?

PARD3 p.Ala934Val (c.2801C>T) is low-frequency (popmax 1.01%, mid) (gnomAD).

What do computational predictors say about PARD3 p.Ala934Val (c.2801C>T)?

AlphaMissense predicts likely benign (score 0.067) — an in-silico prediction, not a clinical call.

PARD3 p.Ala934Val

c.2801C>T · rs16935326 · VCV778036

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 3 submitters

AlphaMissense

likely benign

0.067 · ACMG-weighted

gnomAD v4.1

Rare

low-frequency (popmax 1.01%, mid)

Missense predictors

0/3 damaging

AlphaMissense, REVEL, SaProt

Computational evidence

Protein change
AlphaMissense	0.067	likely benign
REVEL	0.037	moderately benign-leaning
SaProt	LLR -5.86	tolerated
⇒ AlphaMissense, REVEL and SaProt all call this tolerated.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.28	GERP -2.7
Regional constraint	o/e 0.96	unconstrained · MANE · 406 kb · p 0.14 · regional, not allelic
Overall
CADD	4.779	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

⚠ Isoform check: AlphaMissense numbered on a different transcript (AM A937V vs ClinVar A934V) — verify the residue.

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.01% Middle Eastern · 61/6,058 alleles

Filtering AF 0.857% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.835%

Overall 0.22% 3,542/1,613,612 alleles · low-frequency exomes 2,867/1,461,554 · genomes 675/152,058 · joint denominator

Ancestry group	Frequency	1 in
Middle Easterngrpmax	1.01%	99
African / African-American	0.914%	109
Admixed American	0.914%	109
Ashkenazi Jewishnot grpmax-eligible	0.389%	257
Remaining individualsnot grpmax-eligible	0.371%	269
European (non-Finnish)	0.158%	633
East Asian	0.0312%	3,205
South Asian	0.0231%	4,336
Finnishnot grpmax-eligible	0.00313%	32,000

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.Ala934Val
Coding: c.2801C>T
MANE Select: NM_001184785
dbSNP: rs16935326
Type: single nucleotide variant
Location: chr10:34331149 (GRCh38)
Gene constraint: LOEUF 0.61 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 54.37 · 1 PDB
Residue 937 UniProt numbering: the 'interaction with frmd4a' region; the 'disordered' region

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

Similar variants

PARD3 c.2560+10A>G 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
PARD3 p.Ala1337Val 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-ala934val (accessed [today's date]).

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