PDLIM3 p.Arg16=
c.48G>A · rs1345291628 · VCV1743956
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00102%, nfe)
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 -3.3 | GERP -5.2 |
| Overall | ||
| CADD | 5.547 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00102%
European (non-Finnish) · 12/1,177,564 alleles
Filtering AF
0.000543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000429%
Overall
0.000746%
12/1,608,070 alleles · very rare
exomes 10/1,455,888 · genomes 2/152,182 · joint denominator
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.Arg16=
- Coding
- c.48G>A
- MANE Select
- NM_014476
- dbSNP
- rs1345291628
- Type
- single nucleotide variant
- Location
- chr4:185535387 (GRCh38)
- Gene constraint
- LOEUF 1.071 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.98
- Residue 16
- the pdz domain
Similar variants
- PDLIM3 p.Arg16Met Uncertain significance ★★ ⚠ same residue
- PDLIM3 p.Arg16Lys 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
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-arg16 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown