PDLIM3 p.Phe101=
c.303C>T · rs1324560803 · VCV1799129
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00153%, 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 4 | GERP 0.61, phastCons 1 |
| Overall | ||
| CADD | 11.38 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00153%
European (non-Finnish) · 18/1,177,658 alleles
Filtering AF
0.000955%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000788%
Overall
0.00118%
19/1,611,264 alleles · very rare
exomes 17/1,459,088 · genomes 2/152,176 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00153% | 65,425 |
| African / African-American | 0.00134% | 74,856 |
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.Phe101=
- Coding
- c.303C>T
- MANE Select
- NM_014476
- dbSNP
- rs1324560803
- Type
- single nucleotide variant
- Location
- chr4:185523389 (GRCh38)
- Gene constraint
- LOEUF 1.071 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.98
Similar variants
- 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
- PDLIM3 p.Ala38Val 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-phe101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown