KLHL9

kelch like family member 9, the group of BTB domain containing|Kelch like

Basic information

Region (hg38): 9:21329664-21335404

Links

ENSG00000198642 ∙ NCBI:55958 ∙ OMIM:611201 ∙ HGNC:18732 ∙ Uniprot:Q9P2J3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Tourette syndrome (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLHL9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL9 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			5	40	4	49
missense			86	3	2	91
nonsense			2			2
start loss						0
frameshift			3			3
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	98	43	6

Variants in KLHL9

This is a list of pathogenic ClinVar variants found in the KLHL9 region.

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

Position	Type	Phenotype	Significance	ClinVar
9-21333011-A-G		not specified	Uncertain significance (Jun 23, 2021)
9-21333023-G-A		not specified	Uncertain significance (Jul 11, 2023)
9-21333024-T-C			Uncertain significance (Dec 22, 2023)
9-21333025-G-A		not specified	Uncertain significance (Jun 29, 2023)
9-21333025-G-C			Uncertain significance (Jan 11, 2024)
9-21333027-T-C			Benign (Jan 11, 2024)
9-21333030-A-G			Benign (Dec 14, 2023)
9-21333032-G-C			Uncertain significance (Aug 22, 2022)
9-21333034-G-A			Uncertain significance (Sep 19, 2023)
9-21333039-T-C			Likely benign (Aug 27, 2022)
9-21333044-TAGA-T			Uncertain significance (May 22, 2023)
9-21333051-T-G			Likely benign (Oct 07, 2021)
9-21333059-G-T			Uncertain significance (Nov 26, 2022)
9-21333065-C-A			Uncertain significance (Jun 22, 2022)
9-21333068-C-G			Uncertain significance (Jun 27, 2022)
9-21333082-G-T			Uncertain significance (Aug 15, 2023)
9-21333086-G-C			Uncertain significance (May 25, 2021)
9-21333117-T-C			Likely benign (Jul 31, 2021)
9-21333136-T-C			Uncertain significance (Sep 25, 2021)
9-21333141-C-T			Likely benign (Jun 15, 2022)
9-21333158-C-T			Uncertain significance (May 15, 2023)
9-21333177-T-C			Likely benign (Dec 22, 2023)
9-21333193-T-G			Uncertain significance (Mar 18, 2023)
9-21333204-T-C			Likely benign (May 01, 2023)
9-21333212-C-T			Uncertain significance (Mar 13, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL9	protein_coding	protein_coding	ENST00000359039	1	5710

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.820	0.180	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	231	326	0.709	0.0000167	4090
Missense in Polyphen		50	115.6	0.43252		1472
Synonymous	-1.81	137	113	1.22	0.00000554	1188
Loss of Function	3.38	3	18.8	0.159	0.00000118	246

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-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: 0.113

Intolerance Scores

• loftool: 0.410
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.99

Haploinsufficiency Scores

• pHI: 0.183
• hipred: Y
• hipred_score: 0.771
• ghis: 0.601

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.866

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl9

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