# NM_014476.5:c.(?_1)_(93_?)del

https://sugi.bio/variant/pdlim3-c-1

## Summary

**PDLIM3 c.(?_1** is classified **Uncertain significance** in PDLIM3 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-12-30).

**At a glance:** Uncertain significance · review: Single submitter · 1 submitter

## For patients & families {#patients}

This is a change in the PDLIM3 gene that is currently of uncertain significance — a definitive interpretation has not yet been established, submitted by 1 submitter.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

**Support & next steps:** [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PDLIM3](https://sugi.bio/atlas/gene/PDLIM3/) |
| Coding change (HGVS c.) | c.(?_1 |
| MANE Select transcript | [NM_014476](https://www.ncbi.nlm.nih.gov/nuccore/NM_014476) |
| Variant type | Deletion |
| ClinVar | [VCV3256718](https://www.ncbi.nlm.nih.gov/clinvar/variation/3256718/) |

## Gene constraint & dosage {#gene-context}

**PDLIM3** population constraint: LOEUF 1.071, pLI 9.9167e-07, missense-Z 0.74665. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **hypertrophic cardiomyopathy** — Limited (AD)
- **dilated cardiomyopathy** — Disputed (AD)

## Protein context {#protein}


AlphaFold model confidence (whole protein): pLDDT 66.98, 21% of residues very-high.

## Clinical significance {#significance}

**Uncertain significance** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2021-12-30.

**Submitter consensus:** unanimous (1/1 Uncertain significance).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Clinical Genomics Laboratory, Stanford Medicine | Uncertain significance | criteria provided, single submitter | clinical testing | 2021-12-30 |

**Reported phenotype names (ClinVar):** not provided, none provided.

## Similar variants {#similar}

Related PDLIM3 variant pages (same residue, condition, or type): [PDLIM3 c.519-1906_519-1871del](/variant/pdlim3-c-519-minus-1906-519-minus-1871del), [PDLIM3 c.60_93+59del](/variant/pdlim3-c-60-93-plus-59del), [PDLIM3 c.794-9_794-6del](/variant/pdlim3-c-794-minus-9-794-minus-6del), [PDLIM3 c.93+2_93+4del](/variant/pdlim3-c-93-plus-2-93-plus-4del), [PDLIM3 p.Ala225fs](/variant/pdlim3-p-ala225fs), [PDLIM3 p.Ala269fs](/variant/pdlim3-p-ala269fs), [PDLIM3 p.Gln289fs](/variant/pdlim3-p-gln289fs), [PDLIM3 p.Glu106fs](/variant/pdlim3-p-glu106fs).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 3256718). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*