VPS13B

vacuolar protein sorting 13 homolog B, the group of bridge-like lipid transfer protein family

Basic information

Region (hg38): 8:99013265-99877580

Previous symbols: [ "CHS1", "COH1" ]

Links

ENSG00000132549 ∙ NCBI:157680 ∙ OMIM:607817 ∙ HGNC:2183 ∙ Uniprot:Q7Z7G8 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Cohen syndrome (Definitive), mode of inheritance: AR
• Cohen syndrome (Definitive), mode of inheritance: AR
• Cohen syndrome (Strong), mode of inheritance: AR
• Cohen syndrome (Strong), mode of inheritance: AR
• Cohen syndrome (Definitive), mode of inheritance: AR
• Cohen syndrome (Supportive), mode of inheritance: AR
• Cohen syndrome (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cohen syndrome	AR	Allergy/Immunology/Infectious	Though the condition may be frequently recognizable, individuals can have recurrent infections, and antiinfectious prophlyaxis and treatment (including G-CSF for neutropenia), as well as early and aggressive treatment of infections may be beneficial	Allergy/Immunology/Infectious; Craniofacial; Dental; Musculoskeletal; Neurologic; Ophthalmologic	4717588; 671157; 7438489; 7246618; 7166592; 6705238; 3989828; 3656371; 3223494; 9266925; 10466416; 10964838; 12676892; 12730828; 15211651; 15025727; 15141358; 20683995; 20301655; 20921020; 24311531
The condition may be frequently recognizable due to characteristic features, including dysmorphisms

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the VPS13B gene.

• Cohen syndrome (4509 variants)
• not provided (596 variants)
• Inborn genetic diseases (458 variants)
• not specified (193 variants)
• VPS13B-related condition (148 variants)
• Retinitis pigmentosa (4 variants)
• Abnormality of the eye (3 variants)
• Abnormality of the nervous system (3 variants)
• Abnormal brain morphology (2 variants)
• - (2 variants)
• Intellectual disability (2 variants)
• 9 conditions (2 variants)
• Microcephaly (1 variants)
• See cases (1 variants)
• 6 conditions (1 variants)
• 8 conditions (1 variants)
• Pituitary stalk interruption syndrome (1 variants)
• Global developmental delay;High myopia;Retinal dystrophy (1 variants)
• Neutropenia, severe congenital, 1, autosomal dominant (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the VPS13B 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			14	1292	10	1316
missense		3	1702	34	3	1742
nonsense	116	86	4	1	1	208
start loss			1			1
frameshift	195	122	13	2	1	333
inframe indel		2	43			45
splice donor/acceptor (+/-2bp)	22	116	1	2	1	142
splice region		2	93	184	8	287
non coding	2	1	46	428	109	586
Total	335	330	1824	1759	125

Highest pathogenic variant AF is 0.000256

Variants in VPS13B

This is a list of pathogenic ClinVar variants found in the VPS13B region.

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

Position	Type	Phenotype	Significance	ClinVar
8-99013347-T-A		Cohen syndrome	Uncertain significance (Jan 12, 2018)
8-99013352-G-A		Cohen syndrome	Uncertain significance (Sep 23, 2021)
8-99013353-C-G		Cohen syndrome	Uncertain significance (Jan 13, 2018)
8-99013787-A-G		Inborn genetic diseases	Uncertain significance (Mar 12, 2019)
8-99013789-A-T		Cohen syndrome	Uncertain significance (Nov 08, 2022)
8-99013791-G-A		Abnormal brain morphology • not specified • Cohen syndrome	Conflicting classifications of pathogenicity (Jan 29, 2024)
8-99013793-T-A		Cohen syndrome	Uncertain significance (Dec 23, 2021)
8-99013794-G-T		Cohen syndrome	Likely benign (Dec 30, 2023)
8-99013797-G-A		Cohen syndrome	Likely benign (Jun 28, 2023)
8-99013806-A-C		Cohen syndrome	Likely benign (Aug 19, 2022)
8-99013806-A-G		Cohen syndrome	Likely benign (Aug 03, 2021)
8-99013806-A-T		Cohen syndrome • VPS13B-related disorder	Likely benign (Jul 25, 2022)
8-99013807-A-T		Cohen syndrome • VPS13B-related disorder	Uncertain significance (Oct 04, 2023)
8-99013810-C-G		Cohen syndrome	Uncertain significance (Feb 01, 2022)
8-99013810-CC-A		Cohen syndrome	Likely pathogenic (-)
8-99013819-A-T		Cohen syndrome	Uncertain significance (Jun 14, 2022)
8-99013823-G-A		Inborn genetic diseases	Uncertain significance (Oct 30, 2023)
8-99013824-C-T		Cohen syndrome	Likely benign (Mar 23, 2023)
8-99013825-T-C		not specified	Uncertain significance (Aug 17, 2015)
8-99013844-A-G		Cohen syndrome • Inborn genetic diseases • VPS13B-related disorder	Uncertain significance (Dec 05, 2023)
8-99013848-C-A		Cohen syndrome	Uncertain significance (Aug 09, 2022)
8-99013851-A-G		Cohen syndrome	Likely benign (Nov 19, 2020)
8-99013857-G-A		Cohen syndrome	Likely benign (Oct 22, 2023)
8-99013857-G-C		Cohen syndrome	Likely benign (Sep 17, 2022)
8-99013861-G-A		Inborn genetic diseases	Uncertain significance (Apr 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
VPS13B	protein_coding	protein_coding	ENST00000358544	61	864315

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.50e-45	1.00	125352	0	396	125748	0.00158

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.982	1947	2.07e+3	0.939	0.000107	26435
Missense in Polyphen		340	406.8	0.83579		4958
Synonymous	-0.626	772	750	1.03	0.0000396	7801
Loss of Function	5.71	105	190	0.553	0.00000994	2298

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00261	0.00259
Ashkenazi Jewish	0.00179	0.00179
East Asian	0.00164	0.00163
Finnish	0.00353	0.00352
European (Non-Finnish)	0.00148	0.00146
Middle Eastern	0.00164	0.00163
South Asian	0.00145	0.00144
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in protein sorting in post Golgi membrane traffic. {ECO:0000250}.

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.933
• rvis_EVS: -0.61
• rvis_percentile_EVS: 17.5

Haploinsufficiency Scores

• pHI: 0.284
• hipred: Y
• hipred_score: 0.544
• ghis: 0.600

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.349

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Vps13b

Gene ontology

• Biological process: protein transport