KTN1

protein-coding

kinectin 1

Gene summary

This gene encodes an integral membrane protein that is a member of the kinectin protein family. The encoded protein is primarily localized to the endoplasmic reticulum membrane. This protein binds kinesin and may be involved in intracellular organelle motility. This protein also binds translation elongation factor-delta and may be involved in the assembly of the elongation factor-1 complex. Alternate splicing results in multiple transcript variants of this gene. [provided by RefSeq, Aug 2012]

MANE transcript

NM_001079521.2

Inheritance

—

ClinVar variants

U:41B:9

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.26

Max pathogenic AF

—

Genomic locus

chr14:55,559,072-55,701,526

External References & Databases

Ensembl (ENSG00000126777)

Transcript & Mutation Effects

hg38 • Region Span ~142.5 kb

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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 KTN1 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 10

not specifiedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001079521.2. 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	1 clinvar	4 clinvar	10
missense			11 clinvar	2 clinvar	2 clinvar	15
nonsense			3 clinvar			3
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			22 clinvar			22
Total	0	0	41	3	6	50

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 246 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001079521.2	RefSeq	NP_001072989.1	43	MANE Select
ENST00000395314.8	Ensembl	ENSP00000378725.3	43	MANE Select
NM_001079522.2	RefSeq	NP_001072990.1	41	Standard
NM_001271014.2	RefSeq	NP_001257943.1	42	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Glucocorticoid Receptor Pathway
Nuclear Receptors Meta-Pathway
Signal Transduction
Post-translational protein phosphorylation
RHO GTPases activate KTN1

Biological Process

microtubule-based movement
post-translational protein modification
cellular protein metabolic process

Molecular Function

RNA binding
protein binding
kinesin binding
cadherin binding

Cellular Component

endoplasmic reticulum
endoplasmic reticulum lumen
endoplasmic reticulum membrane
integral component of plasma membrane
membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000395314
Coding exons: 43
Length: 142455
Individuals with no LoFs: 125673
Homozygous LoFs: 0
Heterozygous LoFs: 74
Defined: 125747
p: 0.000294

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0232	626	624	1.00	0.0000296	8969
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00037	0.00037	rare
Latino/Admixed American	0.00033	0.00032	rare
Ashkenazi Jewish	0.0010	0.00099	notable
East Asian	0.00044	0.00044	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00029	0.00028	rare
South Asian	0.00010	0.000098	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

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.;

Recessive Scores

pRec: 0.128

Intolerance Scores

LoFtool: 0.0486
RVIS EVS: -0.94
RVIS percentile EVS: 9.41

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.399

Gene Damage Prediction

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