PTK7

protein-coding

protein tyrosine kinase 7 (inactive), the group of I-set domain containing|Receptor tyrosine kinases

Gene summary

This gene encodes a member of the receptor protein tyrosine kinase family of proteins that transduce extracellular signals across the cell membrane. The encoded protein lacks detectable catalytic tyrosine kinase activity, is involved in the Wnt signaling pathway and plays a role in multiple cellular processes including polarity and adhesion. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]

MANE transcript

NM_002821.5

Inheritance

—

ClinVar variants

U:123B:23

Top phenotype

PTK7-related disorder

gnomAD constraint

pLI —, LoF o/e 0.15

Max pathogenic AF

—

Genomic locus

chr6:43,076,307-43,161,719

External References & Databases

Ensembl (ENSG00000112655)

Transcript & Mutation Effects

hg38 • Region Span ~85.4 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PTK7 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 117

not providedTotal: 13

PTK7-related disorderTotal: 12

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_002821.5. 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	4 clinvar	6 clinvar	15
missense			114 clinvar	12 clinvar	1 clinvar	127
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			4 clinvar			4
Total	0	0	123	16	7	146

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 59 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_002821.5	RefSeq	NP_002812.2	20	MANE Select
ENST00000230419.9	Ensembl	ENSP00000230419.4	20	MANE Select
NM_001270398.2	RefSeq	NP_001257327.1	20	Standard
NM_152880.4	RefSeq	NP_690619.1	19	Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / Model	Organism	Observed Phenotype
ptk7b	Danio rerio	Structure: whole organism Quality: increased width abnormal

Gene / Model

Organism

Observed Phenotype

ptk7b

Danio rerio

Structure: whole organism

Quality: increased width

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

establishment of planar polarity
ventricular septum development
axis elongation
protein phosphorylation
cell adhesion

Molecular Function

protein kinase activity
protein binding
ATP binding
coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway

Cellular Component

integral component of plasma membrane
cell-cell junction
focal adhesion

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000481273
Coding exons: 20
Length: 85452
Individuals with no LoFs: 125731
Homozygous LoFs: 0
Heterozygous LoFs: 17
Defined: 125748
p: 0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.24	508	671	0.757	0.0000415	7023
Missense (PolyPhen)		172	288.12	0.59697		3034
Synonymous	-0.552	282	270	1.04	0.0000165	2164
Loss of Function	5.69	8	52.5	0.152	0.00000249	573

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000087	0.000087	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0.00011	0.00011	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000088	0.000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Inactive tyrosine kinase involved in Wnt signaling pathway. Component of both the non-canonical (also known as the Wnt/planar cell polarity signaling) and the canonical Wnt signaling pathway. Functions in cell adhesion, cell migration, cell polarity, proliferation, actin cytoskeleton reorganization and apoptosis. Has a role in embryogenesis, epithelial tissue organization and angiogenesis. {ECO:0000269|PubMed:18471990, ECO:0000269|PubMed:20558616, ECO:0000269|PubMed:20837484, ECO:0000269|PubMed:21103379, ECO:0000269|PubMed:21132015}.;

Recessive Scores

pRec: 0.140

Intolerance Scores

LoFtool: 0.0972
RVIS EVS: -0.77
RVIS percentile EVS: 13.18

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.600

Gene Damage Prediction

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