DENND2A

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

Basic information

Region (hg38): 7:140518419-140673993

Previous symbols: [ "KIAA1277" ]

Links

ENSG00000146966 ∙ NCBI:27147 ∙ OMIM:620120 ∙ HGNC:22212 ∙ Uniprot:Q9ULE3 ∙ 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 DENND2A gene.

• Inborn genetic diseases (38 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND2A 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			38			38
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	0	0

Variants in DENND2A

This is a list of pathogenic ClinVar variants found in the DENND2A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-140519638-C-T		not specified	Uncertain significance (Mar 27, 2023)
7-140519639-C-G		not specified	Uncertain significance (Sep 16, 2021)
7-140521869-C-T		not specified	Uncertain significance (Nov 21, 2022)
7-140521881-C-T		not specified	Uncertain significance (May 16, 2023)
7-140521924-C-T		not specified	Uncertain significance (Jan 30, 2024)
7-140521987-T-G		not specified	Uncertain significance (Jul 13, 2021)
7-140522007-G-A		not specified	Uncertain significance (Nov 07, 2022)
7-140522017-A-G		not specified	Uncertain significance (Oct 27, 2023)
7-140522044-C-T		not specified	Uncertain significance (Dec 08, 2023)
7-140522091-G-T		not specified	Uncertain significance (May 23, 2023)
7-140523397-G-A		not specified	Uncertain significance (Dec 06, 2021)
7-140525764-C-T		not specified	Uncertain significance (Dec 27, 2022)
7-140525774-C-T		not specified	Uncertain significance (Jan 19, 2022)
7-140527331-A-G		not specified	Uncertain significance (Sep 26, 2023)
7-140527382-G-A		not specified	Uncertain significance (Sep 12, 2023)
7-140527392-A-T		not specified	Uncertain significance (Mar 08, 2024)
7-140527401-C-T		not specified	Uncertain significance (Jan 02, 2024)
7-140527428-T-C		not specified	Uncertain significance (Dec 21, 2023)
7-140527472-G-T		not specified	Uncertain significance (Feb 28, 2024)
7-140527473-C-T		not specified	Uncertain significance (Mar 01, 2024)
7-140544632-A-C		not specified	Uncertain significance (Dec 19, 2022)
7-140544633-A-G		not specified	Uncertain significance (Apr 22, 2022)
7-140544691-C-T		not specified	Uncertain significance (Apr 13, 2022)
7-140544711-G-A		not specified	Uncertain significance (Nov 02, 2023)
7-140546882-T-A		not specified	Uncertain significance (Feb 02, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND2A	protein_coding	protein_coding	ENST00000275884	18	155574

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0673	0.933	124772	0	25	124797	0.000100

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.17	506	586	0.864	0.0000356	6532
Missense in Polyphen		149	208.83	0.71351		2337
Synonymous	-0.400	252	244	1.03	0.0000158	2037
Loss of Function	4.77	12	47.4	0.253	0.00000266	548

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000281	0.000279
Ashkenazi Jewish	0.0000993	0.0000993
East Asian	0.00	0.00
Finnish	0.0000937	0.0000928
European (Non-Finnish)	0.0000987	0.0000971
Middle Eastern	0.00	0.00
South Asian	0.000131	0.000131
Other	0.00	0.00

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. May play a role in late endosomes back to trans-Golgi network/TGN transport. {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: 0.394
• rvis_EVS: -0.81
• rvis_percentile_EVS: 12.07

Haploinsufficiency Scores

• pHI: 0.0971
• hipred: N
• hipred_score: 0.492
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.215

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd2a

Gene ontology

• Biological process: protein transport;retrograde transport, endosome to Golgi
• Cellular component: cytosol;actin cytoskeleton
• Molecular function: Rab guanyl-nucleotide exchange factor activity