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.

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.

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						0
missense			41	5		46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	41	5	0

Variants in DENND1C

This is a list of pathogenic ClinVar variants found in the DENND1C region.

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

Position	Type	Phenotype	Significance	ClinVar
19-6467508-C-T		not specified	Uncertain significance (Feb 13, 2023)
19-6467533-C-T		not specified	Uncertain significance (Aug 05, 2024)
19-6467544-C-T		not specified	Likely benign (Jun 11, 2021)
19-6467545-G-A		not specified	Uncertain significance (Apr 19, 2023)
19-6467577-G-T		not specified	Uncertain significance (Nov 10, 2022)
19-6467608-G-A		not specified	Uncertain significance (Jul 16, 2024)
19-6467617-G-A		not specified	Uncertain significance (Oct 22, 2021)
19-6467632-C-T		not specified	Uncertain significance (Sep 24, 2024)
19-6467655-G-T		not specified	Uncertain significance (Aug 31, 2023)
19-6467662-G-A		not specified	Uncertain significance (Nov 23, 2021)
19-6467791-G-T		not specified	Uncertain significance (Jan 16, 2024)
19-6467809-G-T		not specified	Uncertain significance (May 30, 2023)
19-6467812-T-C		not specified	Likely benign (Jun 21, 2023)
19-6467993-C-G		not specified	Uncertain significance (May 17, 2023)
19-6467998-A-C		not specified	Uncertain significance (May 07, 2024)
19-6468054-G-C		not specified	Uncertain significance (Dec 03, 2021)
19-6468094-C-T		not specified	Uncertain significance (Jul 27, 2024)
19-6468249-G-C		not specified	Uncertain significance (Apr 20, 2023)
19-6468305-C-T		not specified	Likely benign (Mar 14, 2023)
19-6468319-A-G		not specified	Uncertain significance (Mar 25, 2024)
19-6468341-C-T		not specified	Uncertain significance (Nov 08, 2024)
19-6468404-A-C		not specified	Uncertain significance (Dec 22, 2023)
19-6468618-G-A		not specified	Uncertain significance (Jun 06, 2022)
19-6468866-T-C		not specified	Uncertain significance (Apr 12, 2024)
19-6468886-C-T		not specified	Uncertain significance (Jun 21, 2023)

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