DENND4C

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

Basic information

Region (hg38): 9:19230434-19374281

Previous symbols: [ "C9orf55B", "C9orf55" ]

Links

ENSG00000137145 ∙ NCBI:55667 ∙ ∙ HGNC:26079 ∙ Uniprot:Q5VZ89 ∙ 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 DENND4C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND4C 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				2		2
missense			97	1		98
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	98	3	0

Variants in DENND4C

This is a list of pathogenic ClinVar variants found in the DENND4C region.

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

Position	Type	Phenotype	Significance	ClinVar
9-19290796-A-G		not specified	Uncertain significance (Jul 28, 2021)
9-19290802-T-G		not specified	Uncertain significance (Feb 21, 2024)
9-19290807-G-C		not specified	Uncertain significance (Jul 20, 2022)
9-19290827-C-T		not specified	Uncertain significance (May 25, 2022)
9-19296027-A-G		not specified	Uncertain significance (Apr 12, 2023)
9-19296096-C-A		not specified	Uncertain significance (Feb 12, 2024)
9-19296159-A-G		not specified	Uncertain significance (Dec 22, 2023)
9-19296195-T-G		not specified	Uncertain significance (May 23, 2024)
9-19296213-C-G		not specified	Uncertain significance (Oct 05, 2021)
9-19298106-C-T		not specified	Uncertain significance (Nov 27, 2023)
9-19299242-A-T		not specified	Uncertain significance (Jun 23, 2023)
9-19300222-G-T		not specified	Uncertain significance (Mar 07, 2024)
9-19300236-G-T		not specified	Uncertain significance (Mar 06, 2023)
9-19305439-A-G		not specified	Uncertain significance (Jul 26, 2021)
9-19305477-C-A		not specified	Uncertain significance (Aug 08, 2023)
9-19305504-C-G		not specified	Uncertain significance (Apr 27, 2022)
9-19305523-T-C		not specified	Uncertain significance (May 09, 2022)
9-19316422-A-G		not specified	Uncertain significance (Sep 22, 2023)
9-19316432-G-T		not specified	Uncertain significance (Apr 12, 2024)
9-19316712-G-A		not specified	Uncertain significance (Dec 14, 2021)
9-19316722-G-C		not specified	Uncertain significance (Dec 21, 2021)
9-19316723-A-G		not specified	Uncertain significance (Nov 18, 2022)
9-19316747-C-G		not specified	Uncertain significance (Sep 20, 2023)
9-19324383-G-A		not specified	Uncertain significance (Apr 24, 2024)
9-19324407-T-G		not specified	Uncertain significance (May 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND4C	protein_coding	protein_coding	ENST00000602925	31	143707

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000398	1.00	125635	0	112	125747	0.000445

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.647	926	872	1.06	0.0000427	12496
Missense in Polyphen		271	345.03	0.78544		5402
Synonymous	-1.98	354	310	1.14	0.0000157	3646
Loss of Function	5.60	25	78.5	0.318	0.00000393	1156

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000781	0.000780
Ashkenazi Jewish	0.00165	0.00159
East Asian	0.000440	0.000435
Finnish	0.000416	0.000416
European (Non-Finnish)	0.000426	0.000422
Middle Eastern	0.000440	0.000435
South Asian	0.000165	0.000163
Other	0.000660	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) activating RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound RAB10 into its active GTP-bound form. Thereby, stimulates SLC2A4/GLUT4 glucose transporter-enriched vesicles delivery to the plasma membrane in response to insulin. {ECO:0000269|PubMed:20937701}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Intolerance Scores

• rvis_EVS: -0.96
• rvis_percentile_EVS: 9.02

Haploinsufficiency Scores

• pHI: 0.386
• hipred: N
• hipred_score: 0.364
• ghis: 0.570

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.162

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd4c
• Phenotype: immune system phenotype; 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); hematopoietic system phenotype

Gene ontology

• Biological process: protein transport;cellular response to insulin stimulus;protein localization to plasma membrane
• Cellular component: cytosol;plasma membrane;cytoplasmic vesicle membrane;retromer complex;insulin-responsive compartment
• Molecular function: Rab guanyl-nucleotide exchange factor activity