DENND2A
Basic information
Region (hg38): 7:140518420-140673993
Previous symbols: [ "KIAA1277" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | 62 | 62 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region | 0 | |||||
non coding | 0 | |||||
Total | 0 | 0 | 62 | 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-A | not specified | Uncertain significance (Aug 27, 2024) | ||
7-140521987-T-G | not specified | Uncertain significance (Jul 13, 2021) | ||
7-140522007-G-A | not specified | Uncertain significance (Nov 07, 2022) | ||
7-140522007-G-C | not specified | Uncertain significance (Dec 03, 2024) | ||
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 (May 24, 2024) | ||
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 (Aug 20, 2024) |
GnomAD
Source:
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:
- 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
- Phenotype
Gene ontology
- Biological process
- protein transport;retrograde transport, endosome to Golgi
- Cellular component
- cytosol;actin cytoskeleton
- Molecular function
- Rab guanyl-nucleotide exchange factor activity