DENND6A

DENN domain containing 6A, the group of DENN domain containing

Basic information

Region (hg38): 3:57625454-57693077

Previous symbols: [ "FAM116A" ]

Links

ENSG00000174839 ∙ NCBI:201627 ∙ ∙ HGNC:26635 ∙ Uniprot:Q8IWF6 ∙ 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 DENND6A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND6A 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	1	0

Variants in DENND6A

This is a list of pathogenic ClinVar variants found in the DENND6A region.

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

Position	Type	Phenotype	Significance	ClinVar
3-57628285-G-A		not specified	Uncertain significance (Aug 20, 2024)
3-57630432-G-T		not specified	Uncertain significance (Dec 03, 2024)
3-57630441-G-C		not specified	Uncertain significance (Oct 03, 2022)
3-57630479-C-T		not specified	Uncertain significance (Oct 25, 2024)
3-57633269-G-A		not specified	Uncertain significance (Feb 16, 2023)
3-57633276-T-C		not specified	Uncertain significance (Nov 07, 2022)
3-57633291-G-C		not specified	Uncertain significance (Dec 19, 2022)
3-57633314-A-G		not specified	Uncertain significance (Jun 28, 2024)
3-57634729-A-T		not specified	Uncertain significance (Sep 24, 2024)
3-57641668-C-T		not specified	Uncertain significance (Nov 24, 2024)
3-57641716-A-C		not specified	Uncertain significance (Mar 07, 2024)
3-57641736-A-G		not specified	Uncertain significance (Mar 27, 2023)
3-57646359-G-C		not specified	Uncertain significance (Feb 08, 2023)
3-57657707-G-C		not specified	Uncertain significance (Nov 27, 2023)
3-57659130-C-G		not specified	Uncertain significance (Apr 25, 2023)
3-57659177-G-A		not specified	Uncertain significance (Dec 07, 2024)
3-57661461-G-A		not specified	Uncertain significance (Jun 21, 2023)
3-57666179-C-A		not specified	Uncertain significance (Aug 17, 2021)
3-57692835-G-A			Likely benign (Jan 01, 2024)
3-57692889-C-T		not specified	Uncertain significance (Jan 03, 2024)
3-57692915-G-A		not specified	Uncertain significance (Apr 15, 2024)
3-57692916-C-A		not specified	Uncertain significance (Apr 15, 2024)
3-57692987-G-A		not specified	Uncertain significance (Nov 18, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND6A	protein_coding	protein_coding	ENST00000311128	20	67633

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00177	0.998	125710	0	38	125748	0.000151

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.07	201	302	0.666	0.0000151	3910
Missense in Polyphen		71	119.14	0.59595		1566
Synonymous	-0.500	113	106	1.06	0.00000504	1136
Loss of Function	4.14	13	41.9	0.310	0.00000244	485

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000336	0.000334
Ashkenazi Jewish	0.00	0.00
East Asian	0.000490	0.000489
Finnish	0.0000466	0.0000462
European (Non-Finnish)	0.000144	0.000141
Middle Eastern	0.000490	0.000489
South Asian	0.000111	0.0000980
Other	0.000188	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Guanine nucleotide exchange factor (GEF) for RAB14. Component of an endocytic recycling pathway that is required for the control of ADAM10 transport, shedding of N-cadherin/CDH2 by ADAM9 or ADAM10 and regulation of cell-cell junctions. Required for RAB14 recruitment to recycling endosomes. {ECO:0000269|PubMed:22595670}.
• Pathway: Vesicle-mediated transport;Membrane Trafficking;Rab regulation of trafficking;RAB GEFs exchange GTP for GDP on RABs (Consensus)

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.264
• hipred: Y
• hipred_score: 0.639
• ghis: 0.568

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dennd6a

Gene ontology

• Biological process: positive regulation of cell-cell adhesion mediated by cadherin
• Cellular component: cytoplasm;cytosol;intracellular membrane-bounded organelle;recycling endosome
• Molecular function: Rab guanyl-nucleotide exchange factor activity