DENND4B

DENN domain containing 4B, the group of DENN domain containing

Basic information

Region (hg38): 1:153929501-153946718

Previous symbols: [ "KIAA0476" ]

Links

ENSG00000198837 ∙ NCBI:9909 ∙ OMIM:619843 ∙ HGNC:29044 ∙ Uniprot:O75064 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• isolated cleft palate (Limited), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DENND4B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND4B 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				12	4	16
missense			78	3		81
nonsense						0
start loss						0
frameshift						0
inframe indel			1	2	1	4
splice donor/acceptor (+/-2bp)						0
splice region				3	1	4
non coding				1	1	2
Total	0	0	79	18	6

Variants in DENND4B

This is a list of pathogenic ClinVar variants found in the DENND4B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-153930369-G-A		DENND4B-related disorder	Likely benign (Jun 05, 2024)
1-153930414-G-C		DENND4B-related disorder	Likely benign (Mar 02, 2023)
1-153930573-T-C		DENND4B-related disorder	Benign (Jun 19, 2019)
1-153930860-G-A		DENND4B-related disorder	Likely benign (Jun 25, 2019)
1-153930964-A-G		not specified	Uncertain significance (Mar 18, 2024)
1-153932214-G-A		not specified	Uncertain significance (Nov 20, 2024)
1-153932235-A-G		not specified	Uncertain significance (Nov 01, 2021)
1-153932266-G-A		not specified	Uncertain significance (Sep 02, 2024)
1-153932287-A-G		DENND4B-related disorder	Likely benign (Mar 05, 2019)
1-153932353-C-T		not specified	Uncertain significance (May 26, 2024)
1-153932382-C-T		not specified	Uncertain significance (Mar 01, 2024)
1-153932401-G-C		not specified	Uncertain significance (May 01, 2022)
1-153932415-C-T		not specified	Uncertain significance (Dec 16, 2022)
1-153932754-C-A		not specified	Uncertain significance (Nov 22, 2023)
1-153932783-G-A		DENND4B-related disorder	Likely benign (Dec 03, 2019)
1-153932867-C-T		not specified	Uncertain significance (Feb 07, 2023)
1-153933207-G-C		not specified	Uncertain significance (Feb 10, 2022)
1-153933212-C-G		not specified	Uncertain significance (Dec 27, 2023)
1-153933231-T-A		not specified	Uncertain significance (Oct 13, 2021)
1-153933241-G-A		not specified	Uncertain significance (Jun 28, 2023)
1-153933255-C-T		not specified	Uncertain significance (May 18, 2023)
1-153933265-G-C		not specified	Uncertain significance (Aug 02, 2023)
1-153933505-C-T		not specified	Uncertain significance (Nov 25, 2024)
1-153933512-G-A		not specified	Uncertain significance (Oct 16, 2023)
1-153933524-G-T		not specified	Uncertain significance (Dec 14, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND4B	protein_coding	protein_coding	ENST00000361217	27	17196

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.991	0.00902	124675	0	17	124692	0.0000682

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.23	607	876	0.693	0.0000562	9335
Missense in Polyphen		218	356.08	0.61222		3790
Synonymous	0.761	342	360	0.949	0.0000206	3335
Loss of Function	6.23	12	67.0	0.179	0.00000327	760

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000906	0.0000906
Ashkenazi Jewish	0.000200	0.000199
East Asian	0.000173	0.000167
Finnish	0.0000991	0.0000928
European (Non-Finnish)	0.0000446	0.0000442
Middle Eastern	0.000173	0.000167
South Asian	0.0000655	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. {ECO:0000269|PubMed:20937701}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• rvis_EVS: -2.46
• rvis_percentile_EVS: 1

Haploinsufficiency Scores

• pHI: 0.388
• hipred: Y
• hipred_score: 0.617
• ghis: 0.579

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.146

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd4b

Gene ontology

• Biological process: regulation of Rab protein signal transduction
• Cellular component: nucleus;Golgi apparatus;cytosol
• Molecular function: Rab guanyl-nucleotide exchange factor activity