PTK7

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

Basic information

Region (hg38): 6:43076307-43161719

Links

ENSG00000112655 ∙ NCBI:5754 ∙ OMIM:601890 ∙ HGNC:9618 ∙ Uniprot:Q13308 ∙ 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 PTK7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PTK7 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			1	3	7	11
missense			37	4	1	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					2	2
non coding					3	3
Total	0	0	38	7	11

Variants in PTK7

This is a list of pathogenic ClinVar variants found in the PTK7 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43076495-G-C		not specified	Uncertain significance (May 18, 2022)
6-43076502-G-T		not specified	Uncertain significance (Aug 22, 2023)
6-43076514-C-T		PTK7-related disorder	Uncertain significance (Oct 24, 2023)
6-43076520-C-G		not specified	Uncertain significance (Jun 21, 2022)
6-43076882-A-G		PTK7-related disorder	Benign (Jan 03, 2020)
6-43076902-G-A		PTK7-related disorder	Benign (Aug 01, 2022)
6-43076969-C-A		PTK7-related disorder	Benign (Sep 18, 2019)
6-43129078-G-A		not specified	Uncertain significance (Feb 07, 2023)
6-43129099-G-A		not specified	Likely benign (Dec 30, 2023)
6-43129135-G-A		not specified	Likely benign (Jun 16, 2024)
6-43129207-C-T		not specified	Uncertain significance (Dec 08, 2023)
6-43129244-A-G		not specified	Uncertain significance (May 01, 2023)
6-43129244-A-T		not specified	Uncertain significance (Jul 05, 2023)
6-43130257-G-A			Benign (Dec 31, 2019)
6-43130318-C-T		not specified	Uncertain significance (May 04, 2023)
6-43130557-A-G		PTK7-related disorder	Likely benign (Mar 29, 2019)
6-43132033-G-A		not specified	Uncertain significance (Apr 24, 2023)
6-43132089-G-A		not specified	Uncertain significance (Dec 19, 2022)
6-43132129-C-T		not specified	Uncertain significance (Jan 20, 2023)
6-43132161-G-A		not specified	Uncertain significance (Nov 13, 2023)
6-43132418-C-T			Benign (May 31, 2018)
6-43132451-G-A		not specified	Uncertain significance (Feb 28, 2023)
6-43132493-C-T			Likely benign (Dec 31, 2019)
6-43132496-C-G		not specified	Uncertain significance (Jan 24, 2024)
6-43132536-G-A		PTK7-related disorder	Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PTK7	protein_coding	protein_coding	ENST00000481273	20	85452

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.997	0.00279	125731	0	17	125748	0.0000676

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.24	508	671	0.757	0.0000415	7023
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000883	0.0000879
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.646
• hipred: Y
• hipred_score: 0.639
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.600

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ptk7
• Phenotype: embryo phenotype; respiratory 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); 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); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); hearing/vestibular/ear phenotype; limbs/digits/tail phenotype; vision/eye phenotype; skeleton phenotype; renal/urinary system phenotype; growth/size/body region phenotype; craniofacial phenotype; cellular phenotype

Zebrafish Information Network

• Gene name: ptk7b
• Affected structure: whole organism
• Phenotype tag: abnormal
• Phenotype quality: increased width

Gene ontology

• Biological process: establishment of planar polarity;ventricular septum development;axis elongation;protein phosphorylation;cell adhesion;signal transduction;positive regulation of neuron projection development;cell migration;actin cytoskeleton reorganization;wound healing;establishment of epithelial cell apical/basal polarity;convergent extension;lung-associated mesenchyme development;coronary vasculature development;cellular response to retinoic acid;cochlea morphogenesis;planar cell polarity pathway involved in neural tube closure;positive regulation of canonical Wnt signaling pathway
• Cellular component: integral component of plasma membrane;cell-cell junction;focal adhesion
• Molecular function: protein kinase activity;protein binding;ATP binding;coreceptor activity involved in Wnt signaling pathway, planar cell polarity pathway