KIF16B

protein-coding

kinesin family member 16B, the group of Kinesins

Gene summary

The protein encoded by this gene is a kinesin-like protein that may be involved in intracellular trafficking. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2010]

Previous symbols:

C20orf23

MANE transcript

NM_024704.5

Inheritance

—

ClinVar variants

U:209B:14

Top phenotype

Prostate cancer

gnomAD constraint

pLI —, LoF o/e 0.64

Max pathogenic AF

—

Genomic locus

chr20:16,272,104-16,573,448

External References & Databases

Ensembl (ENSG00000089177)

Transcript & Mutation Effects

hg38 • Region Span ~301.3 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 KIF16B variants in ClinVar

7 Conditions Cataloged

not specifiedTotal: 227

not providedTotal: 17

Prostate cancerTotal: 2

AutismTotal: 1

Muscular atrophyTotal: 1

KIF16B-related Intellectual DisabilityTotal: 1

See casesTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_024704.5. 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			2 clinvar	2 clinvar	2 clinvar	6
missense			198 clinvar	8 clinvar	2 clinvar	208
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			7 clinvar			7
Total	0	0	209	10	4	223

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 50 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_024704.5	RefSeq	NP_078980.3	26	MANE Select
ENST00000354981.7	Ensembl	ENSP00000347076.2	26	MANE Select
NM_001199865.2	RefSeq	NP_001186794.1	25	Standard
NM_001199866.2	RefSeq	NP_001186795.1	23	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

formation of primary germ layer
regulation of receptor recycling
Golgi to endosome transport
microtubule-based movement
epidermal growth factor receptor signaling pathway

Molecular Function

microtubule motor activity
ATP binding
phosphatidylinositol-3,4,5-trisphosphate binding
microtubule binding
ATP-dependent microtubule motor activity, plus-end-directed

Cellular Component

endosome
early endosome
cytosol
kinesin complex
microtubule

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000408042
Coding exons: 23
Length: 301330
Individuals with no LoFs: 125428
Homozygous LoFs: 0
Heterozygous LoFs: 320
Defined: 125748
p: 0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.10	668	753	0.887	0.0000426	9147
Missense (PolyPhen)		289	360.27	0.80217		4343
Synonymous	1.36	257	286	0.898	0.0000161	2592
Loss of Function	2.68	40	63.0	0.635	0.00000301	811

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0039	0.0038	notable
Latino/Admixed American	0.00048	0.00046	rare
Ashkenazi Jewish	0.0016	0.0016	notable
East Asian	0.0043	0.0042	notable
Finnish	0.00014	0.00014	rare
European (Non-Finnish)	0.0010	0.0010	notable
South Asian	0.00085	0.00082	rare
Other	0.00082	0.00081	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plus end-directed microtubule-dependent motor protein involved in endosome transport and receptor recycling and degradation. Regulates the plus end motility of early endosomes and the balance between recycling and degradation of receptors such as EGF receptor (EGFR) and FGF receptor (FGFR). Regulates the Golgi to endosome transport of FGFR-containing vesicles during early development, a key process for developing basement membrane and epiblast and primitive endoderm lineages during early postimplantation development. {ECO:0000269|PubMed:15882625}.;

Recessive Scores

pRec: 0.111

Intolerance Scores

LoFtool: 0.928
RVIS EVS: 0.44
RVIS percentile EVS: 77.7

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0554

Gene Damage Prediction

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