DCSTAMP

dendrocyte expressed seven transmembrane protein

Basic information

Region (hg38): 8:104339086-104356689

Previous symbols: [ "TM7SF4" ]

Links

ENSG00000164935 ∙ NCBI:81501 ∙ OMIM:605933 ∙ HGNC:18549 ∙ Uniprot:Q9H295 ∙ 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 DCSTAMP gene.

• Inborn genetic diseases (19 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCSTAMP 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			17	2	1	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	17	2	1

Variants in DCSTAMP

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

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

Position	Type	Phenotype	Significance	ClinVar
8-104348556-G-C		not specified	Uncertain significance (Mar 31, 2023)
8-104348676-A-C		not specified	Uncertain significance (Jul 19, 2023)
8-104348747-G-T		not specified	Uncertain significance (Oct 25, 2022)
8-104348755-C-A		not specified	Uncertain significance (Sep 21, 2023)
8-104348773-G-T		not specified	Uncertain significance (Dec 20, 2021)
8-104348778-A-G		not specified	Uncertain significance (May 05, 2023)
8-104348862-G-A		not specified	Uncertain significance (Oct 26, 2021)
8-104348868-G-A		not specified	Uncertain significance (Aug 08, 2023)
8-104348914-T-G		not specified	Uncertain significance (Apr 27, 2022)
8-104348962-A-G		not specified	Uncertain significance (Dec 21, 2023)
8-104349106-A-G		not specified	Uncertain significance (Mar 16, 2022)
8-104349138-G-A		not specified	Likely benign (Feb 10, 2023)
8-104349177-T-C		not specified	Uncertain significance (Nov 29, 2021)
8-104349289-A-G		not specified	Uncertain significance (Jan 23, 2024)
8-104349406-C-T		not specified	Likely benign (May 11, 2022)
8-104349496-A-T		not specified	Uncertain significance (Mar 01, 2023)
8-104349520-C-T		not specified	Uncertain significance (Sep 09, 2021)
8-104354881-A-C		not specified	Uncertain significance (Aug 22, 2023)
8-104354893-A-G			Benign (Feb 24, 2021)
8-104354894-T-A		not specified	Uncertain significance (Oct 29, 2021)
8-104354957-A-C		not specified	Uncertain significance (Sep 01, 2021)
8-104354995-T-C		not specified	Uncertain significance (Feb 15, 2023)
8-104355081-G-A		not specified	Likely benign (Sep 17, 2021)
8-104355169-G-C		not specified	Uncertain significance (Sep 06, 2022)
8-104356132-C-A		not specified	Uncertain significance (Oct 13, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCSTAMP	protein_coding	protein_coding	ENST00000297581	3	17603

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000186	0.693	125604	1	143	125748	0.000573

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.358	234	250	0.936	0.0000131	3062
Missense in Polyphen		56	55.51	1.0088		753
Synonymous	-1.28	118	102	1.16	0.00000571	963
Loss of Function	1.11	11	15.8	0.698	8.57e-7	177

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000753	0.000753
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000441	0.000440
Middle Eastern	0.000109	0.000109
South Asian	0.00245	0.00242
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable cell surface receptor that plays several roles in cellular fusion, cell differentiation, bone and immune homeostasis. Plays a role in TNFSF11-mediated osteoclastogenesis. Cooperates with OCSTAMP in modulating cell-cell fusion in both osteoclasts and foreign body giant cells (FBGCs). Participates in osteoclast bone resorption. Involved in inducing the expression of tartrate-resistant acid phosphatase in osteoclast precursors. Plays a role in haematopoietic stem cell differentiation of bone marrow cells toward the myeloid lineage. Inhibits the development of neutrophilic granulocytes. Plays also a role in the regulation of dendritic cell (DC) antigen presentation activity by controlling phagocytic activity. Involved in the maintenance of immune self-tolerance and avoidance of autoimmune reactions.

Recessive Scores

• pRec: 0.126

Intolerance Scores

• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.25

Haploinsufficiency Scores

• pHI: 0.112
• hipred: N
• hipred_score: 0.123
• ghis: 0.386

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: Dcstamp
• Phenotype: hematopoietic system phenotype; skeleton phenotype; immune system phenotype; cellular phenotype

Gene ontology

• Biological process: negative regulation of cell growth;osteoclast differentiation;positive regulation of macrophage fusion;cellular response to macrophage colony-stimulating factor stimulus;myeloid dendritic cell differentiation;positive regulation of monocyte differentiation;positive regulation of bone resorption;membrane fusion;cellular response to interleukin-4;cellular response to tumor necrosis factor;osteoclast fusion
• Cellular component: endoplasmic reticulum membrane;plasma membrane;cell surface;endosome membrane;integral component of membrane;integral component of endoplasmic reticulum membrane;endoplasmic reticulum-Golgi intermediate compartment membrane
• Molecular function: protein binding