Is PDLIM3 p.Val358= (c.1074C>A) pathogenic?

PDLIM3 p.Val358= (c.1074C>A) is classified Likely benign in PDLIM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2014-04-30). No allele count reported in gnomAD v4.1 (AN 1,614,218).

How common is PDLIM3 p.Val358= (c.1074C>A) in the general population?

PDLIM3 p.Val358= (c.1074C>A) is no allele count reported in gnomAD v4.1 (AN 1,614,218) (gnomAD).

PDLIM3 p.Val358=

c.1074C>A · rs794729095 · VCV201949

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,614,218)

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.41	donor gain · deltas
Pangolin	Δ0.79	gain · loss 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 0.77	GERP -4.6, phastCons 1
Overall
CADD	1.363	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,614,218). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: PDLIM3
Protein: p.Val358=
Coding: c.1074C>A
MANE Select: NM_014476
dbSNP: rs794729095
Type: single nucleotide variant
Location: chr4:185502315 (GRCh38)
Gene constraint: LOEUF 1.071 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 66.98

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

Similar variants

PDLIM3 p.Val358Ile Uncertain significance ★ ⚠ same residue
PDLIM3 p.Ala168Val Uncertain significance ★★ ⚠ same type
PDLIM3 p.Ala171Thr Uncertain significance ★★ ⚠ same type
PDLIM3 p.Ala304Gly Uncertain significance ★★ ⚠ same type
PDLIM3 p.Ala308Thr Uncertain significance ★★ ⚠ same type
PDLIM3 p.Ala308Val Uncertain significance ★★ ⚠ same type
PDLIM3 p.Ala345Thr Uncertain significance ★★ ⚠ same type
PDLIM3 p.Ala347Val 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/pdlim3-p-val358 (accessed [today's date]).

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