DCST1

DC-STAMP domain containing 1, the group of Ring finger proteins

Basic information

Region (hg38): 1:155033824-155050930

Links

ENSG00000163357 ∙ NCBI:149095 ∙ OMIM:619860 ∙ HGNC:26539 ∙ Uniprot:Q5T197 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DCST1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCST1 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			44	4	2	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	44	5	2

Variants in DCST1

This is a list of pathogenic ClinVar variants found in the DCST1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155034070-G-A		not specified	Likely benign (Jun 07, 2023)
1-155034073-C-G		not specified	Uncertain significance (Apr 01, 2024)
1-155034461-C-G		not specified	Uncertain significance (Apr 06, 2023)
1-155034492-G-A		not specified	Uncertain significance (Dec 27, 2023)
1-155034498-C-A		not specified	Uncertain significance (Aug 04, 2023)
1-155034546-G-T		not specified	Uncertain significance (May 17, 2023)
1-155034675-C-A		not specified	Uncertain significance (Mar 25, 2024)
1-155039504-G-C		not specified	Uncertain significance (Oct 25, 2023)
1-155039510-G-A		not specified	Uncertain significance (Jun 07, 2023)
1-155040507-C-G		not specified	Uncertain significance (Oct 03, 2024)
1-155040530-C-T		not specified	Uncertain significance (Mar 11, 2022)
1-155040566-C-T			Benign (Aug 08, 2017)
1-155040568-C-T		not specified	Uncertain significance (Jul 27, 2023)
1-155040569-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-155040580-C-T		not specified	Uncertain significance (Dec 06, 2024)
1-155040590-C-T		not specified	Uncertain significance (Apr 08, 2024)
1-155040618-C-A		not specified	Uncertain significance (Apr 08, 2022)
1-155041427-C-T		not specified	Uncertain significance (Aug 05, 2024)
1-155041461-C-T			Benign (Aug 08, 2017)
1-155041497-A-G		not specified	Uncertain significance (Mar 25, 2024)
1-155041521-C-T		not specified	Uncertain significance (Mar 01, 2023)
1-155041539-G-A		not specified	Likely benign (May 15, 2023)
1-155041569-C-T		not specified	Uncertain significance (Oct 25, 2024)
1-155041733-A-G		not specified	Uncertain significance (Apr 20, 2024)
1-155041744-G-A		not specified	Uncertain significance (Nov 22, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCST1	protein_coding	protein_coding	ENST00000295542	16	17107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.27e-19	0.0355	125635	0	113	125748	0.000449

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.439	400	425	0.940	0.0000258	4540
Missense in Polyphen		93	107.69	0.8636		1190
Synonymous	0.169	167	170	0.984	0.00000952	1423
Loss of Function	0.977	33	39.6	0.832	0.00000221	405

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000826	0.000818
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.000621	0.000607
Middle Eastern	0.000381	0.000381
South Asian	0.000559	0.000555
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: E3 ubiquitin-protein ligase which mediates 'Lys-48'- linked ubiquitination of STAT2 and induces its proteosomal degradation thereby negatively regulating type-I-interferon signaling. {ECO:0000269|PubMed:27782195}.

Recessive Scores

• pRec: 0.0919

Intolerance Scores

• loftool: 0.971
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.72

Haploinsufficiency Scores

• pHI: 0.0760
• hipred: N
• hipred_score: 0.123
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcst1

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;innate immune response;negative regulation of type I interferon-mediated signaling pathway
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: protein binding;metal ion binding;ubiquitin protein ligase activity