KIF21B

protein-coding

kinesin family member 21B, the group of Kinesins|WD repeat domain containing

Gene summary

This gene encodes a member of the kinesin superfamily. Kinesins are ATP-dependent microtubule-based motor proteins that are involved in the intracellular transport of membranous organelles. Single nucleotide polymorphisms in this gene are associated with inflammatory bowel disease and multiple sclerosis. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Nov 2011]

MANE transcript

NM_001252102.2

Inheritance

ClinVar variants

P:1U:309B:28

Top phenotype

neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.31

Max pathogenic AF

—

Genomic locus

chr1:200,969,390-201,023,714

External References & Databases

Ensembl (ENSG00000116852)

Transcript & Mutation Effects

hg38 • Region Span ~54.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

neurodevelopmental disorderSTRONG

Inheritance Pattern: AD

Disease ID:MONDO:0700092

Submitter: PanelApp Australia

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KIF21B variants in ClinVar

13 Conditions Cataloged

not specifiedTotal: 196

not providedTotal: 128

KIF21B-related disorderTotal: 8

Neurodevelopmental disorderTotal: 5

KIF21B-related Neurodevelopmental disorderTotal: 2

Long QT syndromeTotal: 2

Moderate global developmental delayTotal: 1

HypotoniaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001252102.2. 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			3 clinvar	15 clinvar	6 clinvar	24
missense		1 clinvar	272 clinvar	7 clinvar		280
nonsense			10 clinvar			10
start loss						0
frameshift			11 clinvar			11
splice donor/acceptor (+/-2bp)			13 clinvar			13
Total	0	1	309	22	6	338

Highest pathogenic variant AF is 6.842529e-7

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001252102.2	RefSeq	NP_001239031.1	35	MANE Select
ENST00000461742.7	Ensembl	ENSP00000433808.1	35	MANE Select
NM_001252100.2	RefSeq	NP_001239029.1	35	Standard
NM_001252103.2	RefSeq	NP_001239032.1	34	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Membrane Trafficking
Kinesins
Factors involved in megakaryocyte development and platelet production
Hemostasis

Biological Process

microtubule-based movement

Molecular Function

microtubule motor activity
ATP binding
microtubule binding
ATPase activity

Cellular Component

kinesin complex
microtubule
dendrite
growth cone
cytoplasmic vesicle

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000422435
Coding exons: 35
Length: 54309
Individuals with no LoFs: 125622
Homozygous LoFs: 0
Heterozygous LoFs: 126
Defined: 125748
p: 0.000501

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.96	763	1.03e+3	0.741	0.0000697	10650
Missense (PolyPhen)		348	514	0.67705		5404
Synonymous	2.27	373	433	0.861	0.0000300	3269
Loss of Function	6.03	28	89.6	0.313	0.00000518	935

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00086	0.00074	rare
Latino/Admixed American	0.00024	0.00023	rare
Ashkenazi Jewish	0.00083	0.00079	rare
East Asian	0.0013	0.0011	notable
Finnish	0.0010	0.00083	rare
European (Non-Finnish)	0.00052	0.00046	rare
South Asian	0.00010	0.000098	rare
Other	0.00071	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plus-end directed microtubule-dependent motor protein which displays processive activity. Is involved in regulation of microtubule dynamics, synapse function and neuronal morphology, including dendritic tree branching and spine formation. Plays a role in lerning and memory. Involved in delivery of gamma- aminobutyric acid (GABA(A)) receptor to cell surface. {ECO:0000250|UniProtKB:Q9QXL1}.;

Recessive Scores

pRec: 0.119

Intolerance Scores

LoFtool: 0.522
RVIS EVS: -2.91
RVIS percentile EVS: 0.58

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.780

Gene Damage Prediction

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