DENND4A

DENN domain containing 4A, the group of DENN domain containing|MicroRNA protein coding host genes

Basic information

Region (hg38): 15:65658046-65792293

Previous symbols: [ "MYCPBP" ]

Links

ENSG00000174485 ∙ NCBI:10260 ∙ OMIM:600382 ∙ HGNC:24321 ∙ Uniprot:Q7Z401 ∙ 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 DENND4A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND4A 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		1	52	1		54
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	1	52	1	0

Variants in DENND4A

This is a list of pathogenic ClinVar variants found in the DENND4A region.

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

Position	Type	Phenotype	Significance	ClinVar
15-65661891-A-G		not specified	Uncertain significance (Oct 20, 2023)
15-65661928-T-C		not specified	Uncertain significance (Sep 27, 2021)
15-65664587-T-C		not specified	Uncertain significance (Dec 27, 2023)
15-65664612-T-C		not specified	Uncertain significance (Oct 26, 2022)
15-65667682-G-A		not specified	Uncertain significance (Aug 22, 2023)
15-65668023-T-C		not specified	Uncertain significance (Aug 02, 2023)
15-65668056-C-G		not specified	Uncertain significance (Nov 18, 2022)
15-65669923-T-C		not specified	Uncertain significance (Feb 15, 2023)
15-65671797-T-C		not specified	Uncertain significance (Feb 27, 2023)
15-65671817-T-C		not specified	Uncertain significance (Nov 16, 2021)
15-65671829-G-C		not specified	Uncertain significance (May 17, 2023)
15-65671830-C-T		not specified	Likely benign (Jun 02, 2024)
15-65671881-G-C		not specified	Uncertain significance (Oct 12, 2022)
15-65676526-A-T		not specified	Uncertain significance (Jul 09, 2021)
15-65676549-T-A		not specified	Uncertain significance (Jul 11, 2023)
15-65676627-C-A		not specified	Uncertain significance (Feb 27, 2023)
15-65690428-G-T		not specified	Uncertain significance (Dec 27, 2023)
15-65690434-A-G		not specified	Uncertain significance (Mar 29, 2024)
15-65690456-T-C		not specified	Uncertain significance (May 08, 2023)
15-65690510-C-T		not specified	Uncertain significance (Aug 17, 2021)
15-65690774-G-A		not specified	Uncertain significance (May 23, 2023)
15-65691020-G-A		not specified	Uncertain significance (Dec 19, 2022)
15-65691176-T-C		not specified	Uncertain significance (Jan 08, 2024)
15-65691206-G-A		not specified	Likely benign (Oct 13, 2023)
15-65691313-T-G		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND4A	protein_coding	protein_coding	ENST00000443035	31	134248

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.996	0.00373	124611	0	28	124639	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.67	622	939	0.663	0.0000461	12481
Missense in Polyphen		135	284.48	0.47454		3791
Synonymous	2.45	271	327	0.828	0.0000161	3559
Loss of Function	6.89	15	82.6	0.182	0.00000408	1177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000264	0.000255
Ashkenazi Jewish	0.000201	0.000199
East Asian	0.000169	0.000167
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000137	0.000133
Middle Eastern	0.000169	0.000167
South Asian	0.0000690	0.0000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable guanine nucleotide exchange factor (GEF) which may activate RAB10. Promotes the exchange of GDP to GTP, converting inactive GDP-bound Rab proteins into their active GTP- bound form. According to PubMed:8056341, it may bind to ISRE-like element (interferon-stimulated response element) of MYC P2 promoter. {ECO:0000269|PubMed:20937701, ECO:0000269|PubMed:8056341}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.998
• rvis_EVS: -0.92
• rvis_percentile_EVS: 9.77

Haploinsufficiency Scores

• pHI: 0.708
• hipred: Y
• hipred_score: 0.625
• ghis: 0.611

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd4a

Gene ontology

• Biological process: regulation of transcription, DNA-templated
• Cellular component: nucleus;cytosol
• Molecular function: DNA binding;Rab guanyl-nucleotide exchange factor activity