DENND2C

DENN domain containing 2C, the group of DENN domain containing

Basic information

Region (hg38): 1:114582848-114670422

Links

ENSG00000175984 ∙ NCBI:163259 ∙ ∙ HGNC:24748 ∙ Uniprot:Q68D51 ∙ 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 DENND2C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND2C 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					1	1
missense			41			41
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	0	1

Variants in DENND2C

This is a list of pathogenic ClinVar variants found in the DENND2C region.

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

Position	Type	Phenotype	Significance	ClinVar
1-114587391-A-C		not specified	Uncertain significance (Jan 04, 2024)
1-114587459-G-A		not specified	Uncertain significance (May 26, 2024)
1-114587737-G-C		not specified	Uncertain significance (Feb 06, 2023)
1-114587803-C-T		not specified	Uncertain significance (Nov 13, 2024)
1-114587851-G-A		not specified	Uncertain significance (Aug 21, 2024)
1-114587859-C-T		not specified	Uncertain significance (Sep 25, 2024)
1-114594494-G-C		not specified	Uncertain significance (Apr 22, 2022)
1-114594498-C-A		not specified	Uncertain significance (Apr 07, 2022)
1-114594511-C-T		not specified	Uncertain significance (Mar 27, 2023)
1-114594523-A-T		not specified	Uncertain significance (Apr 19, 2023)
1-114594533-G-C		not specified	Uncertain significance (Jan 05, 2022)
1-114595834-C-G		not specified	Uncertain significance (Jan 24, 2023)
1-114595845-T-C		not specified	Uncertain significance (Jun 23, 2023)
1-114595865-T-C		not specified	Uncertain significance (May 04, 2022)
1-114599374-A-G		not specified	Uncertain significance (Jul 30, 2024)
1-114600235-G-A		not specified	Uncertain significance (Nov 15, 2024)
1-114600265-T-C		not specified	Uncertain significance (Feb 06, 2023)
1-114600285-C-T		not specified	Uncertain significance (Jan 04, 2024)
1-114600307-C-T		not specified	Uncertain significance (Mar 28, 2023)
1-114600321-C-T		not specified	Uncertain significance (Jan 18, 2023)
1-114600336-C-T		not specified	Uncertain significance (Aug 17, 2022)
1-114600351-G-A		not specified	Uncertain significance (Jul 10, 2023)
1-114600845-C-T		not specified	Uncertain significance (Nov 22, 2022)
1-114600863-C-T		not specified	Uncertain significance (Sep 26, 2023)
1-114600876-G-A		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND2C	protein_coding	protein_coding	ENST00000393274	18	87575

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.95e-12	1.00	125580	0	166	125746	0.000660

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.382	481	505	0.952	0.0000278	6088
Missense in Polyphen		156	189.84	0.82174		2303
Synonymous	2.41	134	174	0.768	0.00000899	1732
Loss of Function	3.16	27	51.5	0.524	0.00000294	618

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00183	0.00183
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.000275	0.000272
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000338	0.000334
Middle Eastern	0.000275	0.000272
South Asian	0.00169	0.00167
Other	0.000653	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) which may activate RAB9A and RAB9B. 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: 0.102

Intolerance Scores

• loftool: 0.972
• rvis_EVS: 1
• rvis_percentile_EVS: 90.79

Haploinsufficiency Scores

• pHI: 0.623
• hipred: N
• hipred_score: 0.492
• ghis: 0.432

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.313

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd2c
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Molecular function: Rab guanyl-nucleotide exchange factor activity