DNMBP

dynamin binding protein, the group of Dbl family Rho GEFs|BAR and Dbl domain containing

Basic information

Region (hg38): 10:99875577-100009947

Links

ENSG00000107554 ∙ NCBI:23268 ∙ OMIM:611282 ∙ HGNC:30373 ∙ Uniprot:Q6XZF7 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• cataract 48 (Strong), mode of inheritance: AR
• total early-onset cataract (Supportive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Cataract 48	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Ophthalmologic	30290152

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the DNMBP gene.

• Cataract 48 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the DNMBP 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				8	13	21
missense			89	12	8	109
nonsense	1		1			2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			1	2	9	12
Total	1	1	91	22	30

Highest pathogenic variant AF is 0.00000658

Variants in DNMBP

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

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

Position	Type	Phenotype	Significance	ClinVar
10-99877141-C-G		DNMBP-related disorder	Benign (Feb 18, 2019)
10-99877145-G-A		DNMBP-related disorder	Likely benign (Mar 28, 2019)
10-99877160-C-T		DNMBP-related disorder	Benign (Feb 21, 2019)
10-99877204-C-G		not specified	Uncertain significance (Aug 23, 2021)
10-99877205-G-T		not specified	Uncertain significance (Apr 30, 2024)
10-99877247-T-A		not specified	Uncertain significance (Apr 08, 2022)
10-99877297-T-C		not specified	Uncertain significance (Dec 05, 2022)
10-99879821-T-C		not specified	Uncertain significance (Aug 17, 2021)
10-99879859-C-T		DNMBP-related disorder	Benign (Apr 09, 2019)
10-99879891-C-T		not specified	Uncertain significance (Nov 12, 2021)
10-99879911-T-C		DNMBP-related disorder	Likely benign (Jun 25, 2019)
10-99879914-C-T		not specified	Uncertain significance (Jun 01, 2023)
10-99879924-C-T		not specified	Uncertain significance (Oct 25, 2022)
10-99879925-G-A		DNMBP-related disorder	Benign (Apr 05, 2019)
10-99879971-G-A		not specified	Likely benign (Aug 02, 2023)
10-99880001-G-A		not specified	Uncertain significance (Aug 04, 2023)
10-99880005-C-G		not specified	Uncertain significance (Feb 05, 2024)
10-99880039-G-A		Cataract 48 • DNMBP-related disorder	Benign (Jul 30, 2021)
10-99880058-C-T		not specified	Uncertain significance (Dec 20, 2022)
10-99880120-A-C		Cataract 48 • DNMBP-related disorder	Benign (Jul 30, 2021)
10-99880232-C-T		not specified	Uncertain significance (Mar 08, 2024)
10-99880258-G-A		DNMBP-related disorder	Likely benign (Jun 07, 2019)
10-99880299-C-T		not specified	Uncertain significance (Feb 28, 2023)
10-99880301-G-C		not specified	Uncertain significance (Oct 05, 2023)
10-99880314-G-C		not specified	Uncertain significance (Aug 17, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
DNMBP	protein_coding	protein_coding	ENST00000324109	16	134343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.72e-17	1.00	125627	0	121	125748	0.000481

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.651	821	875	0.938	0.0000503	10288
Missense in Polyphen		304	340.9	0.89176		4071
Synonymous	1.18	322	350	0.920	0.0000206	3151
Loss of Function	3.47	38	69.1	0.550	0.00000405	779

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00116	0.00116
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000490	0.000489
Finnish	0.000139	0.0000924
European (Non-Finnish)	0.000458	0.000457
Middle Eastern	0.000490	0.000489
South Asian	0.000915	0.000686
Other	0.000987	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Scaffold protein that links dynamin with actin- regulating proteins. May play a role in membrane trafficking between the cell surface and the Golgi (By similarity). {ECO:0000250}.
• Pathway: Regulation of CDC42 activity (Consensus)

Recessive Scores

• pRec: 0.143

Intolerance Scores

• loftool: 0.893
• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.26

Haploinsufficiency Scores

• pHI: 0.161
• hipred: Y
• hipred_score: 0.637
• ghis: 0.500

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.859

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Dnmbp

Zebrafish Information Network

• Gene name: dnmbp
• Affected structure: renal glomerulus
• Phenotype tag: abnormal
• Phenotype quality: distended

Gene ontology

• Biological process: aging;regulation of Rho protein signal transduction;intracellular signal transduction
• Cellular component: Golgi stack;cytoskeleton;cell junction;synapse
• Molecular function: Rho guanyl-nucleotide exchange factor activity;protein binding