DBNDD1

dysbindin domain containing 1

Basic information

Region (hg38): 16:90004871-90019890

Links

ENSG00000003249 ∙ NCBI:79007 ∙ ∙ HGNC:28455 ∙ Uniprot:Q9H9R9 ∙ 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 DBNDD1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DBNDD1 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	1	0

Variants in DBNDD1

This is a list of pathogenic ClinVar variants found in the DBNDD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-90006339-T-G		not specified	Uncertain significance (Feb 12, 2024)
16-90006369-G-A		not specified	Uncertain significance (Aug 08, 2023)
16-90006385-C-T		not specified	Uncertain significance (Jun 10, 2024)
16-90006400-C-T		not specified	Uncertain significance (Aug 19, 2024)
16-90006417-T-C		not specified	Uncertain significance (Jan 16, 2024)
16-90006418-C-T		not specified	Uncertain significance (Oct 20, 2024)
16-90006427-G-C		not specified	Uncertain significance (Dec 20, 2023)
16-90006459-C-T		not specified	Uncertain significance (Jun 23, 2021)
16-90006474-C-T		not specified	Uncertain significance (Dec 19, 2022)
16-90008821-G-C		not specified	Uncertain significance (Sep 13, 2023)
16-90008910-C-T		not specified	Uncertain significance (Nov 09, 2022)
16-90009304-A-G		not specified	Uncertain significance (Feb 23, 2023)
16-90009313-G-A		not specified	Uncertain significance (Sep 17, 2021)
16-90009322-A-C		not specified	Uncertain significance (Jul 10, 2024)
16-90009342-C-A		not specified	Uncertain significance (Aug 23, 2021)
16-90009355-G-A		not specified	Uncertain significance (Nov 27, 2024)
16-90009383-C-T		not specified	Uncertain significance (Feb 05, 2024)
16-90009406-G-A		not specified	Likely benign (Nov 08, 2021)
16-90009417-C-G		not specified	Uncertain significance (Nov 07, 2022)
16-90009419-C-T		not specified	Uncertain significance (Mar 28, 2022)
16-90009977-G-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DBNDD1	protein_coding	protein_coding	ENST00000304733	4	15264

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000635	0.494	124715	0	8	124723	0.0000321

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.212	108	114	0.944	0.00000734	1138
Missense in Polyphen		46	49.158	0.93576		476
Synonymous	-0.575	61	55.5	1.10	0.00000427	375
Loss of Function	0.465	7	8.46	0.827	5.46e-7	72

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000557	0.0000556
Finnish	0.00	0.00
European (Non-Finnish)	0.0000271	0.0000265
Middle Eastern	0.0000557	0.0000556
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.654
• rvis_EVS: -0.34
• rvis_percentile_EVS: 30.07

Haploinsufficiency Scores

• pHI: 0.302
• hipred: N
• hipred_score: 0.144
• ghis: 0.582

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.274

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dbndd1

Gene ontology

• Cellular component: cytoplasm