DCST2

DC-STAMP domain containing 2

Basic information

Region (hg38): 1:155018520-155033781

Links

ENSG00000163354 ∙ NCBI:127579 ∙ OMIM:619861 ∙ HGNC:26562 ∙ Uniprot:Q5T1A1 ∙ 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 DCST2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCST2 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				2		2
missense			64	3		67
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	5	0

Variants in DCST2

This is a list of pathogenic ClinVar variants found in the DCST2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-155018611-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-155018725-T-C		not specified	Uncertain significance (Jun 13, 2023)
1-155018741-C-G		not specified	Uncertain significance (Apr 22, 2022)
1-155018750-C-T		not specified	Uncertain significance (Feb 01, 2023)
1-155023124-C-T		not specified	Uncertain significance (Feb 06, 2023)
1-155023154-C-T		not specified	Uncertain significance (Jun 11, 2021)
1-155023160-C-T		not specified	Uncertain significance (Nov 15, 2024)
1-155023219-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-155023373-T-G		not specified	Uncertain significance (Sep 15, 2021)
1-155023382-C-T		not specified	Uncertain significance (Aug 08, 2023)
1-155023386-G-C		not specified	Uncertain significance (Jul 06, 2021)
1-155023410-C-G		not specified	Uncertain significance (Oct 24, 2024)
1-155023420-A-T		not specified	Uncertain significance (Feb 21, 2024)
1-155023912-G-T		not specified	Uncertain significance (Aug 27, 2024)
1-155023937-C-A		not specified	Uncertain significance (Jan 23, 2024)
1-155024473-G-A		not specified	Uncertain significance (May 31, 2022)
1-155024505-C-T		not specified	Uncertain significance (Sep 20, 2023)
1-155024520-C-T		not specified	Uncertain significance (Aug 19, 2021)
1-155024521-G-A		not specified	Uncertain significance (Nov 30, 2022)
1-155024524-G-A		not specified	Uncertain significance (May 24, 2024)
1-155024566-G-A		not specified	Uncertain significance (Jun 04, 2024)
1-155024572-G-C		not specified	Uncertain significance (Nov 12, 2024)
1-155024592-G-A		not specified	Uncertain significance (Dec 12, 2023)
1-155026303-T-C		not specified	Uncertain significance (Oct 06, 2022)
1-155026309-C-T		not specified	Uncertain significance (Oct 06, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCST2	protein_coding	protein_coding	ENST00000368424	15	15262

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.82e-12	0.946	125514	0	234	125748	0.000931

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.134	474	466	1.02	0.0000288	4938
Missense in Polyphen		119	122.11	0.9745		1269
Synonymous	0.340	183	189	0.969	0.0000108	1649
Loss of Function	2.16	25	39.7	0.630	0.00000248	375

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00184	0.00183
Ashkenazi Jewish	0.00231	0.00228
East Asian	0.00192	0.00190
Finnish	0.00148	0.00148
European (Non-Finnish)	0.000719	0.000712
Middle Eastern	0.00192	0.00190
South Asian	0.000529	0.000523
Other	0.000659	0.000652

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.907
• rvis_EVS: -0.99
• rvis_percentile_EVS: 8.63

Haploinsufficiency Scores

• pHI: 0.215
• hipred: N
• hipred_score: 0.172
• ghis: 0.527

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.126

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcst2

Gene ontology

• Cellular component: integral component of membrane