KIFBP

kinesin family binding protein, the group of Tetratricopeptide repeat domain containing

Basic information

Region (hg38): 10:68988802-69043544

Previous symbols: [ "KIAA1279", "KIF1BP" ]

Links

ENSG00000198954 ∙ NCBI:26128 ∙ OMIM:609367 ∙ HGNC:23419 ∙ Uniprot:Q96EK5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Goldberg-Shprintzen syndrome (Supportive), mode of inheritance: AR
• Goldberg-Shprintzen syndrome (Definitive), mode of inheritance: AR
• Goldberg-Shprintzen syndrome (Strong), mode of inheritance: AR
• Goldberg-Shprintzen syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Goldberg-Shprintzen megacolon syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Gastrointestinal; Neurologic	7338549; 10874640; 15883926

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KIFBP gene.

• not provided (97 variants)
• Goldberg-Shprintzen megacolon syndrome (55 variants)
• not specified (21 variants)
• Inborn genetic diseases (10 variants)
• KIFBP-related condition (1 variants)
• Peripheral neuropathy (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KIFBP 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			7	15	3	25
missense			56	3	1	60
nonsense	3	1				4
start loss						0
frameshift	2	1				3
inframe indel			1			1
splice donor/acceptor (+/-2bp)		1				1
splice region				3	1	4
non coding			11	11	15	37
Total	5	3	75	29	19

Highest pathogenic variant AF is 0.0000526

Variants in KIFBP

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

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

Position	Type	Phenotype	Significance	ClinVar
10-68988813-G-A		not specified	Likely benign (Jan 04, 2018)
10-68988851-G-T			Uncertain significance (Apr 07, 2020)
10-68988861-G-T		not specified	Uncertain significance (Jun 11, 2021)
10-68988879-C-T			Uncertain significance (May 14, 2021)
10-68988880-G-T		Goldberg-Shprintzen syndrome	Conflicting classifications of pathogenicity (Nov 10, 2022)
10-68988886-T-C			Likely benign (Oct 24, 2022)
10-68988892-G-C		Goldberg-Shprintzen syndrome	Uncertain significance (Jan 12, 2018)
10-68988898-G-A		Goldberg-Shprintzen syndrome	Uncertain significance (Jan 13, 2018)
10-68988900-A-G		not specified • Goldberg-Shprintzen syndrome • KIFBP-related disorder	Benign/Likely benign (Mar 01, 2024)
10-68988910-A-G		Goldberg-Shprintzen syndrome • not specified • KIFBP-related disorder	Conflicting classifications of pathogenicity (Sep 18, 2023)
10-68988931-C-G		Goldberg-Shprintzen syndrome	Uncertain significance (Mar 25, 2024)
10-68988937-CA-C		Goldberg-Shprintzen syndrome	Likely pathogenic (-)
10-68988948-C-G		Goldberg-Shprintzen syndrome	Uncertain significance (Oct 13, 2021)
10-68988953-G-C		Goldberg-Shprintzen syndrome	Uncertain significance (Jan 12, 2018)
10-68988959-C-CTGGAA		Goldberg-Shprintzen syndrome	Pathogenic (-)
10-68988987-C-T			Uncertain significance (Feb 24, 2022)
10-68988990-C-CGCCTGAGGACGAGGATGAGCG		Peripheral neuropathy	Uncertain significance (Aug 22, 2016)
10-68989001-G-T		Goldberg-Shprintzen syndrome	Likely pathogenic (-)
10-68989007-G-A		not specified	Uncertain significance (Apr 19, 2017)
10-68989028-G-A		not specified • Goldberg-Shprintzen syndrome	Benign (Feb 01, 2024)
10-68989034-G-C		Goldberg-Shprintzen syndrome	Benign/Likely benign (Apr 10, 2022)
10-68989041-G-C		not specified	Uncertain significance (Jun 01, 2023)
10-68989063-G-A			Uncertain significance (Aug 31, 2021)
10-68989082-G-T		Goldberg-Shprintzen syndrome	Pathogenic (Jul 01, 2005)
10-68989100-C-T		Goldberg-Shprintzen syndrome	Pathogenic (Jun 15, 2013)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KIFBP	protein_coding	protein_coding	ENST00000361983	7	28252

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0757	0.924	125674	0	73	125747	0.000290

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	255	329	0.775	0.0000159	4074
Missense in Polyphen		68	91.641	0.74202		1174
Synonymous	1.57	104	127	0.822	0.00000597	1184
Loss of Function	3.42	7	25.7	0.272	0.00000116	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00278	0.00278
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000300	0.000299
Middle Eastern	0.000109	0.000109
South Asian	0.000100	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for organization of axonal microtubules, and axonal outgrowth and maintenance during peripheral and central nervous system development. {ECO:0000269|PubMed:16225668, ECO:0000269|PubMed:20621975, ECO:0000269|PubMed:23427148}.

Recessive Scores

• pRec: 0.153

Intolerance Scores

• rvis_EVS: -0.33
• rvis_percentile_EVS: 30.7

Haploinsufficiency Scores

• pHI: 0.144
• hipred: Y
• hipred_score: 0.575
• ghis: 0.578

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Kif1bp
• Phenotype: homeostasis/metabolism phenotype; craniofacial phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype; liver/biliary system phenotype; embryo phenotype; immune system phenotype; vision/eye phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); neoplasm; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); reproductive system phenotype; respiratory system phenotype

Zebrafish Information Network

• Gene name: kif1bp
• Affected structure: neuron
• Phenotype tag: abnormal
• Phenotype quality: disorganized

Gene ontology

• Biological process: mitochondrial transport;nervous system development;cell differentiation
• Cellular component: mitochondrion;cytoskeleton
• Molecular function: protein binding;kinesin binding