DCBLD1

discoidin, CUB and LCCL domain containing 1

Basic information

Region (hg38): 6:117453816-117569858

Links

ENSG00000164465 ∙ NCBI:285761 ∙ ∙ HGNC:21479 ∙ Uniprot:Q8N8Z6 ∙ 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 DCBLD1 gene.

• Inborn genetic diseases (22 variants)
• not provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DCBLD1 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			5	1		6
Total	0	0	21	3	0

Variants in DCBLD1

This is a list of pathogenic ClinVar variants found in the DCBLD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-117482819-G-A		not specified	Uncertain significance (Jan 18, 2022)
6-117482823-T-C			Likely benign (Apr 01, 2022)
6-117482824-G-T		not specified	Uncertain significance (Dec 01, 2023)
6-117482879-A-G		not specified	Uncertain significance (Aug 10, 2021)
6-117503949-C-G		not specified	Uncertain significance (Dec 12, 2023)
6-117503959-C-T		not specified	Uncertain significance (Mar 31, 2023)
6-117503968-C-T		not specified	Uncertain significance (Jun 09, 2022)
6-117519867-G-A		not specified	Likely benign (Nov 02, 2023)
6-117519941-G-A		not specified	Uncertain significance (May 09, 2023)
6-117519947-C-T		not specified	Uncertain significance (Sep 16, 2021)
6-117525416-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-117525417-G-A		not specified	Uncertain significance (Jul 09, 2021)
6-117525431-A-C		not specified	Uncertain significance (Mar 06, 2023)
6-117532320-C-G		not specified	Uncertain significance (Mar 01, 2024)
6-117532338-C-T		not specified	Uncertain significance (Oct 05, 2021)
6-117538813-G-T		not specified	Uncertain significance (Jan 06, 2023)
6-117538833-C-G		not specified	Uncertain significance (Mar 07, 2024)
6-117539262-G-T		not specified	Uncertain significance (Feb 28, 2024)
6-117539336-C-A		not specified	Uncertain significance (Dec 30, 2023)
6-117540668-G-T		not specified	Uncertain significance (Dec 15, 2023)
6-117540740-G-A		not specified	Uncertain significance (Jun 22, 2023)
6-117540939-G-A		not specified	Likely benign (Jan 03, 2022)
6-117541017-C-T		not specified	Uncertain significance (Dec 20, 2021)
6-117543136-C-G		not specified	Uncertain significance (Nov 21, 2022)
6-117543141-G-A		not specified	Uncertain significance (Dec 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DCBLD1	protein_coding	protein_coding	ENST00000296955	15	116042

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.33e-8	0.993	125610	0	138	125748	0.000549

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.622	248	277	0.895	0.0000146	3500
Missense in Polyphen		42	46.447	0.90427		540
Synonymous	-0.0199	103	103	1.00	0.00000593	1035
Loss of Function	2.48	17	32.2	0.528	0.00000179	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000517	0.000517
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000424	0.000381
Finnish	0.00245	0.00245
European (Non-Finnish)	0.000532	0.000519
Middle Eastern	0.000424	0.000381
South Asian	0.000229	0.000229
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.275
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

• pHI: 0.173
• hipred: N
• hipred_score: 0.317
• ghis: 0.557

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.190

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dcbld1

Gene ontology

• Cellular component: integral component of membrane