KBTBD13

kelch repeat and BTB domain containing 13, the group of BTB domain containing

Basic information

Region (hg38): 15:65076746-65079948

Links

ENSG00000234438 ∙ NCBI:390594 ∙ OMIM:613727 ∙ HGNC:37227 ∙ Uniprot:C9JR72 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• nemaline myopathy 6 (Definitive), mode of inheritance: AD
• nemaline myopathy 6 (Moderate), mode of inheritance: AD
• childhood-onset nemaline myopathy (Supportive), mode of inheritance: AD
• nemaline myopathy 6 (Strong), mode of inheritance: AD
• nemaline myopathy 6 (Limited), mode of inheritance: Unknown
• nemaline myopathy 6 (Moderate), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Nemaline myopathy 6	AD	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	Musculoskeletal	11731279; 21104864; 21109227

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KBTBD13 gene.

• Nemaline_myopathy_6 (581 variants)
• Inborn_genetic_diseases (120 variants)
• not_provided (72 variants)
• not_specified (40 variants)
• KBTBD13-related_disorder (17 variants)
• Nemaline_Myopathy,_Dominant (2 variants)
• Actin_accumulation_myopathy (1 variants)
• Colorectal_cancer,_susceptibility_to,_12 (1 variants)
• See_cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KBTBD13 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001101362.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			25	140	6	171
missense	1	3	327	75	14	420
nonsense			15			15
start loss			1	2		3
frameshift			25	5	1	31
splice donor/acceptor (+/-2bp)						0
Total	1	3	393	222	21

Highest pathogenic variant AF is 0.00000441286

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KBTBD13	protein_coding	protein_coding	ENST00000432196	1	3123

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.26e-10	0.0204	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.587	307	279	1.10	0.0000220	2765
Missense in Polyphen		94	92.834	1.0126		1011
Synonymous	-1.44	168	146	1.15	0.0000135	997
Loss of Function	-0.915	13	9.89	1.31	5.12e-7	99

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin ligase complex. {ECO:0000269|PubMed:22542517}.
• Disease: DISEASE: Nemaline myopathy 6 (NEM6) [MIM:609273]: A form of nemaline myopathy characterized by childhood onset of slowly progressive proximal muscle weakness, exercise intolerance, and slow movements with stiff muscles. Patients are unable to run or correct themselves from falling over. {ECO:0000269|PubMed:21109227}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: Post-translational protein modification;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation (Consensus)

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.389

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Kbtbd13

Gene ontology

• Biological process: protein ubiquitination;post-translational protein modification
• Cellular component: cytosol