GeneBe

DENND4C

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

Basic information

Region (hg38): 9:19230435-19374281

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.

  • not_specified (245 variants)
  • not_provided (4 variants)

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. These statistics are base on transcript: NM_001330640.2. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
241
clinvar
5
clinvar
 246
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
1
clinvar
 1
Total 0 0 242 7 0
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
DENND4Cprotein_codingprotein_codingENST00000602925 31143707
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.000003981.0012563501121257470.000445
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.6479268721.060.000042712496
Missense in Polyphen271345.030.785445402
Synonymous-1.983543101.140.00001573646
Loss of Function5.602578.50.3180.000003931156

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0007810.000780
Ashkenazi Jewish0.001650.00159
East Asian0.0004400.000435
Finnish0.0004160.000416
European (Non-Finnish)0.0004260.000422
Middle Eastern0.0004400.000435
South Asian0.0001650.000163
Other0.0006600.000652

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

loftool
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
essential_gene_gene_trap
gene_indispensability_pred
N
gene_indispensability_score
0.162

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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