DENND2B

DENN domain containing 2B, the group of DENN domain containing

Basic information

Region (hg38): 11:8693351-8910951

Previous symbols: [ "ST5" ]

Links

ENSG00000166444 ∙ NCBI:6764 ∙ OMIM:140750 ∙ HGNC:11350 ∙ Uniprot:P78524 ∙ 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 DENND2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND2B 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			70	5	2	77
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding				1	4	5
Total	0	0	70	7	8

Variants in DENND2B

This is a list of pathogenic ClinVar variants found in the DENND2B region.

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

Position	Type	Phenotype	Significance	ClinVar
11-8695456-C-T			Benign (Feb 28, 2019)
11-8696435-C-T		not specified	Uncertain significance (Dec 18, 2023)
11-8696458-T-G		not specified	Uncertain significance (Jun 02, 2023)
11-8696538-G-A		not specified	Uncertain significance (May 23, 2023)
11-8696549-C-T		not specified	Uncertain significance (Sep 09, 2021)
11-8696643-C-T		not specified	Uncertain significance (Feb 22, 2024)
11-8697528-C-T		not specified	Uncertain significance (Sep 15, 2021)
11-8697564-C-T		not specified	Uncertain significance (Oct 12, 2021)
11-8697620-G-A		not specified	Uncertain significance (Nov 20, 2023)
11-8699217-T-G		not specified	Uncertain significance (Nov 09, 2021)
11-8699279-G-A			Likely benign (Jun 20, 2018)
11-8699369-G-C		not specified	Uncertain significance (Dec 20, 2023)
11-8702644-A-G			Likely benign (Mar 01, 2023)
11-8702645-C-T		not specified	Uncertain significance (Dec 14, 2021)
11-8702647-C-T		not specified	Uncertain significance (May 17, 2023)
11-8702689-C-G		not specified	Uncertain significance (May 24, 2023)
11-8707189-C-T			Benign (Dec 31, 2019)
11-8707207-G-A		not specified	Uncertain significance (Feb 13, 2024)
11-8707806-G-A		not specified	Uncertain significance (Apr 17, 2023)
11-8707838-G-A		not specified	Uncertain significance (Jun 29, 2022)
11-8707850-C-T		not specified	Uncertain significance (May 24, 2023)
11-8708304-T-G			Benign (May 01, 2022)
11-8711140-G-A		not specified	Uncertain significance (Dec 15, 2022)
11-8711224-C-T		not specified	Uncertain significance (Mar 24, 2023)
11-8711231-G-C		not specified	Uncertain significance (Aug 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND2B	protein_coding	protein_coding	ENST00000534127	19	217601

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000362	125736	0	12	125748	0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	553	691	0.800	0.0000438	7355
Missense in Polyphen		174	251.42	0.69208		2706
Synonymous	0.381	270	278	0.971	0.0000171	2316
Loss of Function	6.15	6	55.4	0.108	0.00000346	591

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000119	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.0000622	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB9A and RAB9B. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP- bound form. May be involved in cytoskeletal organization and tumorogenicity. Isoform 1 seems to be involved in a signaling transduction pathway leading to activation of MAPK1/ERK2. Isoform 3 may block ERK2 activation stimulated by ABL1. Isoform 3 may alter cell morphology and cell growth. {ECO:0000269|PubMed:10229203, ECO:0000269|PubMed:20937701, ECO:0000269|PubMed:9632734}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.145

Intolerance Scores

• loftool: 0.390
• rvis_EVS: -0.72
• rvis_percentile_EVS: 14.26

Haploinsufficiency Scores

• pHI: 0.341
• hipred: Y
• hipred_score: 0.851
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.771

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: St5

Gene ontology

• Molecular function: Rab guanyl-nucleotide exchange factor activity