DENND6B

DENN domain containing 6B, the group of DENN domain containing

Basic information

Region (hg38): 22:50309030-50327012

Previous symbols: [ "FAM116B" ]

Links

ENSG00000205593 ∙ NCBI:414918 ∙ ∙ HGNC:32690 ∙ Uniprot:Q8NEG7 ∙ 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 DENND6B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND6B 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		1
missense			57	1		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	57	2	0

Variants in DENND6B

This is a list of pathogenic ClinVar variants found in the DENND6B region.

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

Position	Type	Phenotype	Significance	ClinVar
22-50312159-C-G		not specified	Uncertain significance (Mar 21, 2023)
22-50312207-G-T		not specified	Uncertain significance (Dec 16, 2023)
22-50312210-C-T		not specified	Uncertain significance (Dec 18, 2023)
22-50312222-T-C		not specified	Uncertain significance (Jan 08, 2024)
22-50312236-G-A		not specified	Uncertain significance (Feb 08, 2025)
22-50312257-C-G		not specified	Uncertain significance (Apr 21, 2022)
22-50312257-C-T		not specified	Uncertain significance (Mar 30, 2024)
22-50312353-C-T		not specified	Uncertain significance (Feb 22, 2023)
22-50312354-G-A		not specified	Uncertain significance (Jan 17, 2025)
22-50312567-C-T		not specified	Uncertain significance (Jul 05, 2022)
22-50312579-G-A		not specified	Uncertain significance (Jun 17, 2024)
22-50312588-G-A		not specified	Uncertain significance (Aug 02, 2021)
22-50313041-T-C		not specified	Uncertain significance (Jan 21, 2025)
22-50313080-T-G		not specified	Uncertain significance (Mar 07, 2025)
22-50313099-G-C		not specified	Uncertain significance (Oct 03, 2022)
22-50313099-G-T		not specified	Uncertain significance (Nov 25, 2024)
22-50313101-G-A		not specified	Uncertain significance (Sep 10, 2024)
22-50313678-C-A		not specified	Uncertain significance (Nov 14, 2023)
22-50313678-C-T		not specified	Uncertain significance (Mar 25, 2024)
22-50313679-G-A		not specified	Uncertain significance (Dec 03, 2021)
22-50313699-T-C		not specified	Uncertain significance (Dec 11, 2024)
22-50313710-C-T		not specified	Likely benign (Mar 28, 2024)
22-50313836-G-A		not specified	Uncertain significance (Mar 29, 2022)
22-50313845-C-T		not specified	Uncertain significance (Dec 04, 2024)
22-50313860-G-A		not specified	Uncertain significance (Jun 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND6B	protein_coding	protein_coding	ENST00000413817	20	18031

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.79e-9	0.985	124393	0	33	124426	0.000133

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.862	280	324	0.865	0.0000207	3716
Missense in Polyphen		72	87.32	0.82455		1010
Synonymous	-0.0185	134	134	1.00	0.00000865	1131
Loss of Function	2.32	19	33.5	0.567	0.00000159	392

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000251	0.000245
Ashkenazi Jewish	0.000104	0.0000996
East Asian	0.000115	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.000132	0.000124
Middle Eastern	0.000115	0.000111
South Asian	0.000295	0.000294
Other	0.000166	0.000165

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for RAB14. Also has some, lesser GEF activity towards RAB35. {ECO:0000269|PubMed:22595670}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Intolerance Scores

• rvis_EVS: -0.95
• rvis_percentile_EVS: 9.27

Haploinsufficiency Scores

• pHI: 0.186
• hipred: N
• hipred_score: 0.414
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd6b

Gene ontology

• Cellular component: cytosol;recycling endosome
• Molecular function: Rab guanyl-nucleotide exchange factor activity