DMBT1

deleted in malignant brain tumors 1, the group of Scavenger receptor cysteine rich domain containing

Basic information

Region (hg38): 10:122560665-122643736

Links

ENSG00000187908 ∙ NCBI:1755 ∙ OMIM:601969 ∙ HGNC:2926 ∙ Uniprot:Q9UGM3 ∙ 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 DMBT1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DMBT1 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				52	3	55
missense			150	26	15	191
nonsense						0
start loss						0
frameshift				2		2
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2	1	3
non coding				3	2	5
Total	0	0	150	83	20

Variants in DMBT1

This is a list of pathogenic ClinVar variants found in the DMBT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-122560784-C-A		DMBT1-related disorder	Likely benign (Mar 13, 2023)
10-122570905-C-G		DMBT1-related disorder	Benign (Jun 05, 2019)
10-122572320-C-T		DMBT1-related disorder	Likely benign (Oct 31, 2022)
10-122572358-G-A		not specified	Uncertain significance (Feb 05, 2024)
10-122573759-G-C		not specified	Uncertain significance (May 01, 2022)
10-122574140-G-A			Benign (Jul 15, 2020)
10-122576407-T-C		not specified	Uncertain significance (Dec 28, 2023)
10-122576410-G-A		not specified	Uncertain significance (Sep 22, 2022)
10-122576410-G-C		not specified	Uncertain significance (Mar 28, 2024)
10-122576466-C-G		not specified	Uncertain significance (Oct 14, 2021)
10-122576477-G-C		not specified	Uncertain significance (Nov 17, 2022)
10-122576594-G-A		not specified	Uncertain significance (Jun 17, 2022)
10-122576624-G-A		not specified	Uncertain significance (Apr 22, 2024)
10-122576635-C-T		not specified	Likely benign (May 28, 2024)
10-122576654-G-T		not specified	Uncertain significance (Nov 30, 2022)
10-122576674-C-A		not specified	Uncertain significance (Aug 04, 2023)
10-122576695-G-C		not specified	Uncertain significance (Aug 04, 2023)
10-122577829-C-T		not specified	Uncertain significance (May 27, 2022)
10-122578744-C-T		not specified	Uncertain significance (Feb 09, 2022)
10-122579622-A-G		not specified	Uncertain significance (May 03, 2023)
10-122579635-G-A		not specified	Uncertain significance (Jan 22, 2024)
10-122579653-G-A		not specified	Likely benign (Oct 04, 2022)
10-122579665-G-A		not specified	Uncertain significance (Oct 10, 2023)
10-122579668-C-A		not specified	Uncertain significance (Feb 22, 2023)
10-122579690-C-A		not specified	Uncertain significance (Apr 08, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DMBT1	protein_coding	protein_coding	ENST00000368909	53	83072

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.48e-63	2.07e-8	123608	48	1091	124747	0.00458

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-2.19	1217	1.02e+3	1.19	0.0000600	15402
Missense in Polyphen		430	414.78	1.0367		6457
Synonymous	-5.52	550	408	1.35	0.0000245	4856
Loss of Function	0.824	101	110	0.915	0.00000662	1554

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00462	0.00454
Ashkenazi Jewish	0.0254	0.0117
East Asian	0.0119	0.0115
Finnish	0.0103	0.0103
European (Non-Finnish)	0.00300	0.00243
Middle Eastern	0.0119	0.0115
South Asian	0.00893	0.00600
Other	0.00869	0.00612

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be considered as a candidate tumor suppressor gene for brain, lung, esophageal, gastric, and colorectal cancers. May play roles in mucosal defense system, cellular immune defense and epithelial differentiation. May play a role as an opsonin receptor for SFTPD and SPAR in macrophage tissues throughout the body, including epithelial cells lining the gastrointestinal tract. May play a role in liver regeneration. May be an important factor in fate decision and differentiation of transit-amplifying ductular (oval) cells within the hepatic lineage. Required for terminal differentiation of columnar epithelial cells during early embryogenesis. May function as a binding protein in saliva for the regulation of taste sensation. Binds to HIV-1 envelope protein and has been shown to both inhibit and facilitate viral transmission. Displays a broad calcium-dependent binding spectrum against both Gram-positive and Gram-negative bacteria, suggesting a role in defense against bacterial pathogens. Binds to a range of poly- sulfated and poly-phosphorylated ligands which may explain its broad bacterial-binding specificity. Inhibits cytoinvasion of S.enterica. Associates with the actin cytoskeleton and is involved in its remodeling during regulated exocytosis. Interacts with pancreatic zymogens in a pH-dependent manner and may act as a Golgi cargo receptor in the regulated secretory pathway of the pancreatic acinar cell. {ECO:0000269|PubMed:10485905, ECO:0000269|PubMed:11007786, ECO:0000269|PubMed:11751412, ECO:0000269|PubMed:16796526, ECO:0000269|PubMed:17548659, ECO:0000269|PubMed:17709527, ECO:0000269|PubMed:19189310, ECO:0000269|PubMed:9288095}.
• Disease: DISEASE: Glioma (GLM) [MIM:137800]: Gliomas are benign or malignant central nervous system neoplasms derived from glial cells. They comprise astrocytomas and glioblastoma multiforme that are derived from astrocytes, oligodendrogliomas derived from oligodendrocytes and ependymomas derived from ependymocytes. Note=The gene represented in this entry is involved in disease pathogenesis. Homozygous deletions may be the predominant mechanism of DMBT1 inactivation playing a role in carcinogenesis. DMBT1 is deleted in medulloblastoma and glioblastoma cell lines; point mutations have also been reported in patients with glioma. A loss or reduction of DMBT1 expression has been seen in esophageal, gastric, lung and colorectal carcinomas as well.
• Pathway: Salivary secretion - Homo sapiens (human);Surfactant metabolism;Metabolism of proteins (Consensus)

Intolerance Scores

• loftool: 0.999
• rvis_EVS: 4.22
• rvis_percentile_EVS: 99.72

Haploinsufficiency Scores

• pHI: 0.254
• hipred: N
• hipred_score: 0.273

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.624

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dmbt1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; digestive/alimentary phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); embryo phenotype; renal/urinary system phenotype; immune system phenotype

Gene ontology

• Biological process: pattern recognition receptor signaling pathway;receptor-mediated endocytosis;multicellular organism development;protein transport;viral process;epithelial cell differentiation;induction of bacterial agglutination;cellular protein metabolic process;innate immune response;defense response to Gram-negative bacterium;defense response to Gram-positive bacterium;defense response to virus
• Cellular component: extracellular region;extracellular space;cytoplasm;external side of plasma membrane;extrinsic component of membrane;phagocytic vesicle membrane;extracellular matrix;zymogen granule membrane;extracellular exosome
• Molecular function: scavenger receptor activity;protein binding;signaling pattern recognition receptor activity;zymogen binding;calcium-dependent protein binding