PRICKLE3

protein-coding

prickle planar cell polarity protein 3, the group of Prickle planar cell polarity proteins|LIM domain containing

Gene summary

LIM domain only 6 is a three LIM domain-containing protein. The LIM domain is a cysteine-rich sequence motif that binds zinc atoms to form a specific protein-binding interface for protein-protein interactions. [provided by RefSeq, Jul 2008]

Previous symbols:

LMO6

MANE transcript

NM_006150.5

Inheritance

ClinVar variants

U:113B:5

Top phenotype

Leber optic atrophy

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chrX:49,174,802-49,186,528

External References & Databases

Ensembl (ENSG00000012211)

Transcript & Mutation Effects

hg38 • Region Span ~11.7 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Leber hereditary optic neuropathyLIMITED

Inheritance Pattern: XL

Disease ID:MONDO:0010788

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PRICKLE3 variants in ClinVar

4 Conditions Cataloged

not specifiedTotal: 92

not providedTotal: 7

Leber optic atrophyTotal: 1

Progressive sensorineural hearing impairmentTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006150.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			5 clinvar	2 clinvar		7
missense			102 clinvar	3 clinvar		105
nonsense			2 clinvar			2
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	113	5	0	118

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 28 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006150.5	RefSeq	NP_006141.2	9	MANE Select
ENST00000599218.6	Ensembl	ENSP00000470248.1	9	MANE Select
NM_001307979.2	RefSeq	NP_001294908.1	7	Standard
ENST00000376317.4	Ensembl	ENSP00000365494.4	4	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Wnt signaling pathway - Homo sapiens (human)

Biological Process

multicellular organism development
biological_process
cell projection organization

Molecular Function

protein binding
zinc ion binding

Cellular Component

cellular_component
nucleus
cytoplasm
centrosome
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000376317
Coding exons: 9
Length: 11695
Individuals with no LoFs: 125733
Homozygous LoFs: 5
Heterozygous LoFs: 4
Defined: 125742
p: 0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.19	232	289	0.803	0.0000275	3948
Missense (PolyPhen)		48	77.652	0.61815		1171
Synonymous	0.885	98	110	0.893	0.0000101	1238
Loss of Function	3.04	3	16.2	0.185	0.00000121	283

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000038	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000073	0.000054	rare
Finnish	0.000063	0.000046	rare
European (Non-Finnish)	0.000074	0.000053	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Involved in the planar cell polarity (PCP) pathway that is essential for the polarization of epithelial cells during morphogenetic processes, including gastrulation and neurulation (By similarity). PCP is maintained by two molecular modules, the global and the core modules, PRICKLE3 being part of the core module (By similarity). Distinct complexes of the core module segregate to opposite sides of the cell, where they interact with the opposite complex in the neighboring cell at or near the adherents junctions (By similarity). Involved in the organization of the basal body (By similarity). Involved in cilia growth and positioning (By similarity). {ECO:0000250|UniProtKB:A8WH69}.;

Recessive Scores

pRec: 0.112

Intolerance Scores

LoFtool: 0.210
RVIS EVS: -0.36
RVIS percentile EVS: 29.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.693