DENND1C

DENN domain containing 1C, the group of DENN domain containing

Basic information

Region (hg38): 19:6467207-6482557

Previous symbols: [ "FAM31C" ]

Links

ENSG00000205744

∙ NCBI:79958 ∙ OMIM:613634 ∙ HGNC:26225 ∙ Uniprot:Q8IV53 ∙ 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 DENND1C gene.

not_specified (108 variants)
not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND1C gene is commonly pathogenic or not. These statistics are base on transcript: NM_000024898.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			99 clinvar	8 clinvar		107
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	99	10	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND1C	protein_coding	protein_coding	ENST00000381480	23	15351

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000133	1.00	124576	0	64	124640	0.000257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.760	391	436	0.897	0.0000243	5076
Missense in Polyphen		116	155.01	0.74832		1874
Synonymous	0.715	173	185	0.933	0.0000107	1643
Loss of Function	3.08	16	35.9	0.446	0.00000167	419

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000355	0.000285
Ashkenazi Jewish	0.0000995	0.0000994
East Asian	0.0000564	0.0000556
Finnish	0.0000966	0.0000928
European (Non-Finnish)	0.000424	0.000398
Middle Eastern	0.0000564	0.0000556
South Asian	0.000199	0.000196
Other	0.000346	0.000330

dbNSFP

Source: dbNSFP

Function: FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB8A, RAB13 and RAB35. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP-bound form. {ECO:0000269|PubMed:20154091, 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: 0.935
rvis_EVS: 1.25
rvis_percentile_EVS: 93.47

Haploinsufficiency Scores

pHI: 0.122
hipred: N
hipred_score: 0.321
ghis: 0.460

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.0666

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Dennd1c
Phenotype: skeleton phenotype;

Gene ontology

Biological process: endocytosis;endocytic recycling
Cellular component: cytosol;clathrin-coated vesicle;intracellular membrane-bounded organelle
Molecular function: Rab guanyl-nucleotide exchange factor activity;Rab GTPase binding;phosphatidylinositol phosphate binding