Is PDLIM3 p.Val302= (c.906C>T) pathogenic?

PDLIM3 p.Val302= (c.906C>T) is classified Benign in PDLIM3 (ClinVar, Multiple submitters, 6 submitters; last evaluated 2026-02-04). Common (popmax 85.6%, nfe) — too common for a highly-penetrant pathogenic allele; Associated with hypertrophic cardiomyopathy.

What condition is associated with PDLIM3 p.Val302= (c.906C>T)?

PDLIM3 p.Val302= (c.906C>T) is associated with hypertrophic cardiomyopathy, dilated cardiomyopathy (ClinVar).

PDLIM3 p.Val302=

Q: How common is PDLIM3 p.Val302= (c.906C>T) in the general population?

PDLIM3 p.Val302= (c.906C>T) is common (popmax 85.6%, nfe) — too common for a highly-penetrant pathogenic allele (gnomAD).

c.906C>T · rs4635850 · VCV138675

Benign Multiple submitters

Classification

Benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 6 submitters

gnomAD v4.1

Common

common (popmax 85.6%, nfe) — too common for a highly-penetrant pathogenic allele

Conditions

hypertrophic cardiomyopathy

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -5.3	GERP -5.1
Overall
CADD	0.069	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 85.6% European (non-Finnish) · 1,009,595/1,179,386 alleles

Filtering AF 85.5% ClinGen BA1/BS1 input FAF95, joint · FAF99 85.4%

Overall 81.8% 1,320,144/1,613,280 alleles · common

Ancestry group	Frequency	1 in
Amishnot grpmax-eligible	88%	1
Finnishnot grpmax-eligible	87.6%	1
European (non-Finnish)grpmax	85.6%	1
East Asian	81.9%	1
Remaining individualsnot grpmax-eligible	78.8%	1
Ashkenazi Jewishnot grpmax-eligible	75.3%	1
Admixed American	75.1%	1
South Asian	75.1%	1
Middle Eastern	67.9%	1
African / African-American	37.3%	3

Amish shows a higher raw frequency than the grpmax group above it. gnomAD excludes bottlenecked groups — Finnish, Ashkenazi Jewish, Amish and “Remaining individuals” — from grpmax, because founder effects make their frequencies unrepresentative for filtering. The table is sorted by frequency, so an excluded group can sit above the grpmax row.

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: PDLIM3
Protein: p.Val302=
Coding: c.906C>T
MANE Select: NM_014476
dbSNP: rs4635850
Type: single nucleotide variant
Location: chr4:185502483 (GRCh38)
Gene constraint: LOEUF 1.071 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.98
Residue 302: the lim zinc-binding domain

Full PDLIM3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

hypertrophic cardiomyopathy — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: dilated cardiomyopathy

Similar variants

PDLIM3 p.Val302Ile Uncertain significance ★ ⚠ same residue
PDLIM3 p.Ala168Val Uncertain significance ★★ ⚠ same condition
PDLIM3 p.Ala171Thr Uncertain significance ★★ ⚠ same condition
PDLIM3 p.Ala304Gly Uncertain significance ★★ ⚠ same condition
PDLIM3 p.Ala308Thr Uncertain significance ★★ ⚠ same condition
PDLIM3 p.Ala308Val Uncertain significance ★★ ⚠ same condition
PDLIM3 p.Ala345Thr Uncertain significance ★★ ⚠ same condition
PDLIM3 p.Ala347Val Uncertain significance ★★ ⚠ 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/pdlim3-p-val302 (accessed [today's date]).

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