DENND2D

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

Basic information

Region (hg38): 1:111185968-111204535

Links

ENSG00000162777 ∙ NCBI:79961 ∙ OMIM:615111 ∙ HGNC:26192 ∙ Uniprot:Q9H6A0 ∙ 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 DENND2D gene.

• Inborn genetic diseases (22 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND2D 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			21	1		22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	1	0

Variants in DENND2D

This is a list of pathogenic ClinVar variants found in the DENND2D region.

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

Position	Type	Phenotype	Significance	ClinVar
1-111188148-C-G		not specified	Uncertain significance (Feb 02, 2024)
1-111188250-C-A		not specified	Uncertain significance (Jun 29, 2023)
1-111188251-T-C		not specified	Uncertain significance (Dec 02, 2021)
1-111188277-G-T		not specified	Uncertain significance (Jun 06, 2022)
1-111188298-G-A		not specified	Uncertain significance (Jan 05, 2022)
1-111188353-C-T		not specified	Uncertain significance (Jul 12, 2023)
1-111188704-T-C		not specified	Uncertain significance (Apr 27, 2023)
1-111188729-G-A		not specified	Uncertain significance (Feb 01, 2023)
1-111192316-T-C		not specified	Uncertain significance (Dec 03, 2021)
1-111194620-G-A		not specified	Uncertain significance (Nov 12, 2021)
1-111194660-A-G		not specified	Uncertain significance (Oct 06, 2021)
1-111197235-G-A		not specified	Uncertain significance (Jan 11, 2023)
1-111197246-C-A		not specified	Uncertain significance (Nov 17, 2022)
1-111197928-G-A		not specified	Uncertain significance (Jun 06, 2023)
1-111198702-C-T		not specified	Uncertain significance (Mar 11, 2024)
1-111198703-G-A		not specified	Uncertain significance (Apr 08, 2022)
1-111198715-C-G		not specified	Uncertain significance (Oct 05, 2021)
1-111198726-C-T		not specified	Uncertain significance (Jul 25, 2023)
1-111198727-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-111198742-G-A		not specified	Uncertain significance (Nov 08, 2022)
1-111199634-G-T		not specified	Uncertain significance (Aug 17, 2022)
1-111199652-C-T		not specified	Uncertain significance (Jan 26, 2022)
1-111199669-C-T		not specified	Likely benign (Dec 14, 2021)
1-111199693-A-G		not specified	Uncertain significance (Oct 20, 2023)
1-111199789-T-G		not specified	Uncertain significance (Jan 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND2D	protein_coding	protein_coding	ENST00000357640	12	17362

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000814	0.999	125444	2	302	125748	0.00121

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.13	216	268	0.806	0.0000149	3076
Missense in Polyphen		77	119.03	0.64687		1379
Synonymous	-0.282	105	101	1.04	0.00000572	891
Loss of Function	2.99	10	26.6	0.376	0.00000139	302

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000528	0.000518
Ashkenazi Jewish	0.00150	0.00149
East Asian	0.0000549	0.0000544
Finnish	0.00424	0.00417
European (Non-Finnish)	0.00148	0.00145
Middle Eastern	0.0000549	0.0000544
South Asian	0.000533	0.000523
Other	0.00115	0.00114

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: 0.100

Intolerance Scores

• loftool: 0.746
• rvis_EVS: -0.29
• rvis_percentile_EVS: 33.34

Haploinsufficiency Scores

• pHI: 0.0863
• hipred: N
• hipred_score: 0.455
• ghis: 0.518

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.483

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd2d
• Phenotype: skeleton 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; growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Cellular component: nucleoplasm;cytosol
• Molecular function: protein binding;Rab guanyl-nucleotide exchange factor activity