KTN1

kinectin 1

Basic information

Region (hg38): 14:55559072-55701526

Links

ENSG00000126777 ∙ ∙ OMIM:600381 ∙ HGNC:6467 ∙ Uniprot:Q86UP2 ∙ 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 KTN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KTN1 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	4	5
missense				2	2	4
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	0	3	6

Variants in KTN1

This is a list of pathogenic ClinVar variants found in the KTN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-55617996-A-G			Likely benign (Dec 31, 2019)
14-55628008-C-A			Benign (Dec 31, 2019)
14-55629968-A-C			Benign (Jun 29, 2018)
14-55639190-C-T			Benign (Apr 09, 2018)
14-55640948-G-C			Benign (Feb 25, 2018)
14-55647013-A-G			Benign (Mar 29, 2018)
14-55661569-A-G			Likely benign (Jul 13, 2018)
14-55671640-C-T			Benign (Feb 25, 2018)
14-55673204-A-G			Likely benign (Aug 01, 2022)
14-55678416-T-C			Benign (Jun 29, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KTN1	protein_coding	protein_coding	ENST00000395314	43	142455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00645	0.994	125673	0	74	125747	0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0232	626	624	1.00	0.0000296	8969
Missense in Polyphen		130	158.93	0.81799		2625
Synonymous	-0.231	221	217	1.02	0.0000103	2277
Loss of Function	6.68	24	93.9	0.256	0.00000447	1239

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000698	0.000697
Ashkenazi Jewish	0.00101	0.000993
East Asian	0.000442	0.000435
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000287	0.000281
Middle Eastern	0.000442	0.000435
South Asian	0.000105	0.0000980
Other	0.000493	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for kinesin thus involved in kinesin-driven vesicle motility. Accumulates in integrin-based adhesion complexes (IAC) upon integrin aggregation by fibronectin.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway;Signal Transduction;Post-translational protein phosphorylation;RHO GTPases activate KTN1;Post-translational protein modification;Metabolism of proteins;Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs);RHO GTPase Effectors;Signaling by Rho GTPases;TNFalpha (Consensus)

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.0486
• rvis_EVS: -0.94
• rvis_percentile_EVS: 9.41

Haploinsufficiency Scores

• pHI: 0.390
• hipred: Y
• hipred_score: 0.548
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.399

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ktn1
• Phenotype: normal phenotype

Gene ontology

• Biological process: microtubule-based movement;post-translational protein modification;cellular protein metabolic process
• Cellular component: endoplasmic reticulum;endoplasmic reticulum lumen;endoplasmic reticulum membrane;integral component of plasma membrane;membrane;integral component of membrane
• Molecular function: RNA binding;protein binding;kinesin binding;cadherin binding