DEPP1

DEPP autophagy regulator 1

Basic information

Region (hg38): 10:44970980-44978809

Previous symbols: [ "C10orf10" ]

Links

ENSG00000165507 ∙ NCBI:11067 ∙ OMIM:611309 ∙ HGNC:23355 ∙ Uniprot:Q9NTK1 ∙ 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 DEPP1 gene.

• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DEPP1 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	1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	0	0	1

Variants in DEPP1

This is a list of pathogenic ClinVar variants found in the DEPP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-44971843-C-T		not specified	Uncertain significance (Mar 24, 2023)
10-44977483-G-A		not specified	Uncertain significance (Oct 27, 2021)
10-44977730-T-C			Benign (Aug 03, 2017)
10-44977769-G-A		not specified	Likely benign (Aug 10, 2021)
10-44977783-C-T		not specified	Likely benign (Nov 05, 2021)
10-44978006-C-T		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DEPP1	protein_coding	protein_coding	ENST00000298295	1	7830

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.336	0.497	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.169	128	134	0.959	0.00000790	1363
Missense in Polyphen		39	40.118	0.97214		355
Synonymous	-0.429	58	54.0	1.07	0.00000305	478
Loss of Function	0.657	0	0.503	0.00	2.19e-8	6

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a critical modulator of FOXO3-induced autophagy via increased cellular ROS. {ECO:0000269|PubMed:24530860, ECO:0000269|PubMed:25261981, ECO:0000269|PubMed:28545464}.

Recessive Scores

• pRec: 0.0890

Intolerance Scores

• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.66

Haploinsufficiency Scores

• pHI: 0.0471
• hipred: N
• hipred_score: 0.123
• ghis: 0.476

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Depp1
• Phenotype: normal phenotype

Gene ontology

• Biological process: autophagy;regulation of autophagy
• Cellular component: cytoplasm;mitochondrion;peroxisome