KLHL13

kelch like family member 13, the group of BTB domain containing|Kelch like

Basic information

Region (hg38): X:117897813-118117340

Previous symbols: [ "BKLHD2", "KIAA1309" ]

Links

ENSG00000003096 ∙ NCBI:90293 ∙ OMIM:300655 ∙ HGNC:22931 ∙ Uniprot:Q9P2N7 ∙ 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 KLHL13 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL13 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				6	3	9
missense			9	1		10
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	7	3

Variants in KLHL13

This is a list of pathogenic ClinVar variants found in the KLHL13 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-117898954-T-C		not specified	Uncertain significance (Apr 22, 2024)
X-117898961-G-C		not specified	Uncertain significance (Nov 03, 2023)
X-117899103-C-T			Likely benign (Apr 01, 2022)
X-117899319-C-T			Likely benign (Apr 01, 2022)
X-117899320-G-A		not specified	Uncertain significance (Jul 13, 2022)
X-117901897-G-A			Likely benign (Aug 01, 2022)
X-117909563-C-T			Benign (Dec 20, 2017)
X-117909566-A-G			Likely benign (Apr 01, 2023)
X-117909589-G-A		not specified	Uncertain significance (Aug 17, 2022)
X-117909608-C-G			Benign (Dec 20, 2018)
X-117909659-C-T			Likely benign (Apr 05, 2018)
X-117909774-G-A		not specified	Uncertain significance (Jan 31, 2022)
X-117909885-G-C		not specified	Uncertain significance (Jul 28, 2021)
X-117909941-G-A			Benign (Dec 31, 2019)
X-117919523-C-A		not specified	Uncertain significance (May 09, 2023)
X-117919684-T-C		not specified	Uncertain significance (Jan 17, 2024)
X-117920314-A-G			Likely benign (Apr 01, 2022)
X-117920363-T-G		not specified	Uncertain significance (Mar 16, 2022)
X-117945498-T-C		not specified	Uncertain significance (Jan 23, 2023)
X-117945517-C-T		not specified	Uncertain significance (Apr 29, 2024)
X-118028424-C-T			Likely benign (Jan 01, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL13	protein_coding	protein_coding	ENST00000539496	8	219528

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0350	0.964	125725	4	6	125735	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.20	157	256	0.612	0.0000195	4356
Missense in Polyphen		46	96.313	0.47761		1544
Synonymous	0.733	83	91.9	0.903	0.00000710	1237
Loss of Function	2.78	6	19.1	0.313	0.00000147	346

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000246
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000624	0.0000440
Middle Eastern	0.00	0.00
South Asian	0.0000525	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for mitotic progression and cytokinesis. The BCR(KLHL9-KLHL13) E3 ubiquitin ligase complex mediates the ubiquitination of AURKB and controls the dynamic behavior of AURKB on mitotic chromosomes and thereby coordinates faithful mitotic progression and completion of cytokinesis. {ECO:0000269|PubMed:14528312, ECO:0000269|PubMed:17543862, ECO:0000269|PubMed:19995937}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);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;Aurora B signaling (Consensus)

Recessive Scores

• pRec: 0.0909

Intolerance Scores

• loftool: 0.514
• rvis_EVS: -0.23
• rvis_percentile_EVS: 37.32

Haploinsufficiency Scores

• pHI: 0.266
• hipred: Y
• hipred_score: 0.866
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.968

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl13

Gene ontology

• Biological process: cell cycle;protein ubiquitination;regulation of cytokinesis;post-translational protein modification;cell division
• Cellular component: cytosol;midbody;Cul3-RING ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity