PDLIM7

PDZ and LIM domain 7, the group of LIM domain containing|PDZ domain containing

Basic information

Region (hg38): 5:177483393-177497606

Links

ENSG00000196923 ∙ NCBI:9260 ∙ OMIM:605903 ∙ HGNC:22958 ∙ Uniprot:Q9NR12 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the PDLIM7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PDLIM7 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous					3	3
missense			37		2	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	37	0	5

Variants in PDLIM7

This is a list of pathogenic ClinVar variants found in the PDLIM7 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-177483687-T-C		not specified	Uncertain significance (Feb 13, 2024)
5-177483688-T-C		not specified	Uncertain significance (Mar 07, 2024)
5-177483716-G-A			Benign (Dec 31, 2019)
5-177483968-A-T		not specified	Uncertain significance (Nov 10, 2022)
5-177484081-T-C		not specified	Uncertain significance (Apr 17, 2023)
5-177484088-C-T		not specified	Uncertain significance (Oct 10, 2023)
5-177484100-T-C		not specified	Uncertain significance (Jun 16, 2024)
5-177484126-G-A		not specified	Uncertain significance (Oct 22, 2021)
5-177484155-C-A			Benign (Jun 13, 2018)
5-177488115-C-T		not specified	Uncertain significance (Sep 16, 2021)
5-177489394-G-A		not specified	Uncertain significance (Jan 19, 2024)
5-177489402-T-C		not specified	Uncertain significance (Feb 27, 2024)
5-177489421-C-T		not specified	Uncertain significance (Sep 22, 2023)
5-177489433-C-T		not specified	Uncertain significance (Mar 18, 2024)
5-177489464-G-A			Benign (Dec 31, 2019)
5-177489510-G-A		not specified	Uncertain significance (Jul 06, 2021)
5-177489516-G-A		not specified	Uncertain significance (Mar 18, 2024)
5-177489541-T-C		not specified	Uncertain significance (Jun 22, 2023)
5-177489550-T-C		not specified	Uncertain significance (Sep 22, 2023)
5-177489551-G-C		not specified	Uncertain significance (May 09, 2023)
5-177489554-C-T			Benign (Dec 31, 2019)
5-177489558-G-A		not specified	Uncertain significance (Apr 16, 2024)
5-177489568-C-G		not specified	Uncertain significance (Apr 13, 2023)
5-177489577-C-T		not specified	Uncertain significance (Aug 02, 2023)
5-177489597-G-A		not specified	Uncertain significance (Jan 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PDLIM7	protein_coding	protein_coding	ENST00000355841	12	14213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.708	0.292	125712	0	15	125727	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.731	247	282	0.877	0.0000187	2947
Missense in Polyphen		96	124.17	0.77313		1254
Synonymous	-1.26	134	117	1.15	0.00000844	887
Loss of Function	3.50	4	21.6	0.186	0.00000101	260

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000125
Ashkenazi Jewish	0.000102	0.0000992
East Asian	0.00	0.00
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.0000461	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.000216	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May function as a scaffold on which the coordinated assembly of proteins can occur. May play a role as an adapter that, via its PDZ domain, localizes LIM-binding proteins to actin filaments of both skeletal muscle and nonmuscle tissues. Involved in both of the two fundamental mechanisms of bone formation, direct bone formation (e.g. embryonic flat bones mandible and cranium), and endochondral bone formation (e.g. embryonic long bone development). Plays a role during fracture repair. Involved in BMP6 signaling pathway (By similarity). {ECO:0000250, ECO:0000269|PubMed:11874232, ECO:0000269|PubMed:7929196}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;EBV LMP1 signaling;Developmental Biology;Signaling events regulated by Ret tyrosine kinase;RET signaling;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.130

Intolerance Scores

• loftool: 0.152
• rvis_EVS: -0.66
• rvis_percentile_EVS: 16.02

Haploinsufficiency Scores

• pHI: 0.105
• hipred: Y
• hipred_score: 0.775
• ghis: 0.592

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.917

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Pdlim7
• Phenotype: homeostasis/metabolism phenotype; growth/size/body region phenotype; respiratory system phenotype; immune system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Zebrafish Information Network

• Gene name: pdlim7
• Affected structure: atrioventricular valve
• Phenotype tag: abnormal
• Phenotype quality: aplastic

Gene ontology

• Biological process: ossification;receptor-mediated endocytosis;axon guidance;actin cytoskeleton organization;positive regulation of osteoblast differentiation
• Cellular component: stress fiber;ruffle;nucleus;cytosol;cell-cell adherens junction;focal adhesion;actin cytoskeleton
• Molecular function: protein binding;metal ion binding