DENND10

DENN domain containing 10, the group of DENN domain containing

Basic information

Region (hg38): 10:119104086-119137984

Previous symbols: [ "FAM45A" ]

Links

ENSG00000119979 ∙ NCBI:404636 ∙ ∙ HGNC:31793 ∙ Uniprot:Q8TCE6 ∙ 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 DENND10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DENND10 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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	0	0

Variants in DENND10

This is a list of pathogenic ClinVar variants found in the DENND10 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-119104147-C-A		not specified	Uncertain significance (Oct 26, 2024)
10-119104150-C-T		not specified	Uncertain significance (Dec 21, 2023)
10-119104186-T-C		not specified	Uncertain significance (Nov 09, 2021)
10-119104189-G-C		not specified	Uncertain significance (Feb 07, 2023)
10-119108016-C-T		not specified	Uncertain significance (Feb 15, 2023)
10-119108126-A-T		not specified	Uncertain significance (Dec 04, 2024)
10-119108132-A-G		not specified	Likely benign (Jul 27, 2024)
10-119108159-A-C		not specified	Uncertain significance (Dec 21, 2023)
10-119117566-T-C		not specified	Uncertain significance (May 24, 2023)
10-119117638-G-A		not specified	Uncertain significance (Jun 18, 2021)
10-119117665-A-G		not specified	Uncertain significance (Dec 14, 2021)
10-119120359-G-A		not specified	Uncertain significance (Mar 07, 2023)
10-119120412-G-A		not specified	Uncertain significance (Dec 09, 2023)
10-119120449-C-T		not specified	Uncertain significance (Mar 27, 2023)
10-119123483-T-C		not specified	Uncertain significance (Nov 21, 2022)
10-119123507-C-T		not specified	Uncertain significance (Aug 04, 2023)
10-119123527-C-T		not specified	Uncertain significance (Jan 31, 2023)
10-119123536-G-A		not specified	Uncertain significance (Aug 11, 2022)
10-119129581-A-G		not specified	Uncertain significance (Nov 12, 2021)
10-119129605-T-C		not specified	Uncertain significance (May 25, 2022)
10-119132535-C-G		not specified	Uncertain significance (Jan 02, 2024)
10-119132598-C-T		not specified	Uncertain significance (Apr 04, 2023)
10-119132608-A-G		not specified	Uncertain significance (Jul 09, 2021)
10-119136589-C-G		not specified	Uncertain significance (Aug 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DENND10	protein_coding	protein_coding	ENST00000361432	9	33899

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.46e-8	0.652	125693	2	53	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.855	155	188	0.824	0.00000927	2334
Missense in Polyphen		23	41.289	0.55705		569
Synonymous	0.947	62	72.2	0.858	0.00000417	687
Loss of Function	1.19	14	19.7	0.710	0.00000110	222

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000298	0.000272
Finnish	0.000337	0.000323
European (Non-Finnish)	0.000233	0.000220
Middle Eastern	0.000298	0.000272
South Asian	0.000473	0.000392
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0704

Intolerance Scores

• loftool: 0.366
• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.276
• ghis: 0.493

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam45a