DCBLD2

discoidin, CUB and LCCL domain containing 2

Basic information

Region (hg38): 3:98795940-98901695

Links

ENSG00000057019 ∙ NCBI:131566 ∙ OMIM:608698 ∙ HGNC:24627 ∙ Uniprot:Q96PD2 ∙ 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 DCBLD2 gene.

• Inborn genetic diseases (28 variants)
• not provided (2 variants)
• not specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCBLD2 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			26	1		27
nonsense			1			1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	28	2	1

Variants in DCBLD2

This is a list of pathogenic ClinVar variants found in the DCBLD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-98799502-T-C		not specified	Uncertain significance (Aug 02, 2021)
3-98799515-G-T		not specified	Uncertain significance (Dec 19, 2022)
3-98799553-T-C		not specified	Uncertain significance (Feb 06, 2023)
3-98799566-C-T		not specified	Uncertain significance (Dec 16, 2022)
3-98799682-G-A		not specified	Uncertain significance (Dec 05, 2022)
3-98799686-T-C		DCBLD2-related disorder	Likely benign (Feb 25, 2022)
3-98799701-C-T		not specified	Uncertain significance (Jan 23, 2024)
3-98799724-C-T		not specified	Uncertain significance (Sep 20, 2023)
3-98799814-A-G		not specified	Uncertain significance (Sep 17, 2021)
3-98800636-C-T		not specified	Uncertain significance (Jul 14, 2022)
3-98800650-C-T		not specified	Uncertain significance (Jan 04, 2022)
3-98800651-G-A		not specified	Uncertain significance (Sep 16, 2021)
3-98801639-T-G		not specified	Uncertain significance (Mar 16, 2023)
3-98808138-A-G		not specified	Uncertain significance (Dec 21, 2023)
3-98811473-G-T		not specified	Uncertain significance (Jul 20, 2021)
3-98811485-G-A		not specified	Uncertain significance (Jul 20, 2021)
3-98811506-T-C		not specified	Uncertain significance (Nov 03, 2022)
3-98811551-C-T		not specified	Uncertain significance (Jul 19, 2023)
3-98817808-T-C			Benign (Oct 19, 2017)
3-98817819-C-T		DCBLD2-related disorder	Likely benign (Jan 03, 2023)
3-98817870-T-C		not specified	Uncertain significance (Jul 14, 2021)
3-98819255-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-98819268-C-T		not specified	Uncertain significance (Jun 21, 2021)
3-98819276-G-A		not specified	Uncertain significance (Oct 12, 2022)
3-98819372-G-A		not specified	Uncertain significance (Jul 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCBLD2	protein_coding	protein_coding	ENST00000326840	16	105749

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0954	0.905	124624	0	30	124654	0.000120

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.953	360	415	0.868	0.0000211	4994
Missense in Polyphen		73	113.67	0.64223		1339
Synonymous	0.0877	149	150	0.991	0.00000783	1538
Loss of Function	4.09	9	35.2	0.256	0.00000149	467

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000188	0.000187
Ashkenazi Jewish	0.00	0.00
East Asian	0.000173	0.000167
Finnish	0.00	0.00
European (Non-Finnish)	0.000107	0.000106
Middle Eastern	0.000173	0.000167
South Asian	0.000330	0.000294
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Pathway: EGFR1 (Consensus)

Recessive Scores

• pRec: 0.100

Intolerance Scores

• loftool: 0.299
• rvis_EVS: 0.71
• rvis_percentile_EVS: 85.76

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.443
• ghis: 0.495

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.657

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcbld2
• Phenotype: cellular phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; skeleton phenotype

Zebrafish Information Network

• Gene name: dcbld2
• Affected structure: thrombocyte
• Phenotype tag: abnormal
• Phenotype quality: aggregated

Gene ontology

• Biological process: negative regulation of cell growth;intracellular receptor signaling pathway;wound healing
• Cellular component: integral component of plasma membrane;cell surface
• Molecular function: protein binding