KIF16B

kinesin family member 16B, the group of Kinesins

Basic information

Region (hg38): 20:16272104-16573448

Previous symbols: [ "C20orf23" ]

Links

ENSG00000089177 ∙ NCBI:55614 ∙ OMIM:618171 ∙ HGNC:15869 ∙ Uniprot:Q96L93 ∙ 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 KIF16B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIF16B 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	2	3
missense			89	4	2	95
nonsense						0
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	90	5	4

Variants in KIF16B

This is a list of pathogenic ClinVar variants found in the KIF16B region.

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

Position	Type	Phenotype	Significance	ClinVar
20-16273309-A-G		not specified	Uncertain significance (Jun 06, 2023)
20-16273372-C-T		not specified	Uncertain significance (Sep 30, 2021)
20-16273399-C-T		not specified	Uncertain significance (Nov 09, 2021)
20-16312355-CAG-C		Muscular atrophy	Uncertain significance (Mar 17, 2021)
20-16312378-T-C		not specified	Uncertain significance (Jul 15, 2021)
20-16312412-C-A		not specified	Uncertain significance (Apr 13, 2022)
20-16335978-C-T		not specified	Uncertain significance (May 09, 2022)
20-16356340-A-C			Uncertain significance (Mar 11, 2021)
20-16356344-C-T		not specified	Uncertain significance (Feb 10, 2022)
20-16356353-C-A		not specified	Uncertain significance (Mar 01, 2024)
20-16356379-T-C			Uncertain significance (Jun 01, 2017)
20-16356395-T-C		not specified	Uncertain significance (Jun 01, 2023)
20-16356401-T-C			Uncertain significance (Nov 04, 2020)
20-16356439-C-T		not specified	Uncertain significance (Dec 08, 2023)
20-16367180-G-A		not specified	Uncertain significance (Jun 11, 2021)
20-16367357-G-A		not specified	Uncertain significance (Apr 08, 2024)
20-16367450-A-G		not specified	Likely benign (Dec 26, 2023)
20-16367496-C-T		not specified	Uncertain significance (Feb 02, 2024)
20-16367512-G-C			Likely benign (Mar 01, 2023)
20-16367550-A-G		not specified	Uncertain significance (Aug 30, 2021)
20-16367634-G-A		not specified	Uncertain significance (Aug 12, 2022)
20-16367645-A-G		not specified	Uncertain significance (Dec 21, 2023)
20-16367647-G-T		not specified	Uncertain significance (May 03, 2023)
20-16367663-T-C		not specified	Uncertain significance (Feb 13, 2024)
20-16367717-G-A		not specified	Uncertain significance (May 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIF16B	protein_coding	protein_coding	ENST00000408042	23	301330

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.10e-19	0.979	125428	0	320	125748	0.00127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.10	668	753	0.887	0.0000426	9147
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00439	0.00430
Ashkenazi Jewish	0.00159	0.00159
East Asian	0.00432	0.00425
Finnish	0.000139	0.000139
European (Non-Finnish)	0.00102	0.00101
Middle Eastern	0.00432	0.00425
South Asian	0.000847	0.000817
Other	0.000818	0.000815

dbNSFP

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}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Kinesins;Factors involved in megakaryocyte development and platelet production;Hemostasis;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.928
• rvis_EVS: 0.44
• rvis_percentile_EVS: 77.7

Haploinsufficiency Scores

• pHI: 0.444
• hipred: N
• hipred_score: 0.327
• ghis: 0.487

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0554

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kif16b
• Phenotype: embryo 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)

Gene ontology

• Biological process: formation of primary germ layer;regulation of receptor recycling;Golgi to endosome transport;microtubule-based movement;epidermal growth factor receptor signaling pathway;endoderm development;fibroblast growth factor receptor signaling pathway;receptor catabolic process;early endosome to late endosome transport;cellular response to interferon-gamma
• Cellular component: endosome;early endosome;cytosol;kinesin complex;microtubule;early endosome membrane;phagocytic vesicle
• Molecular function: microtubule motor activity;ATP binding;phosphatidylinositol-3,4,5-trisphosphate binding;microtubule binding;ATP-dependent microtubule motor activity, plus-end-directed;ATPase activity;Rab GTPase binding;phosphatidylinositol-3-phosphate binding;phosphatidylinositol-3,4-bisphosphate binding;phosphatidylinositol-3,5-bisphosphate binding