KLHL6

kelch like family member 6, the group of Kelch like|BTB domain containing

Basic information

Region (hg38): 3:183487551-183555706

Links

ENSG00000172578 ∙ NCBI:89857 ∙ OMIM:614214 ∙ HGNC:18653 ∙ Uniprot:Q8WZ60 ∙ 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 KLHL6 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL6 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			16	1		17
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	16	1	0

Variants in KLHL6

This is a list of pathogenic ClinVar variants found in the KLHL6 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-183491937-A-G		not specified	Uncertain significance (Jun 07, 2024)
3-183491961-A-C		not specified	Uncertain significance (May 30, 2024)
3-183492018-A-C		not specified	Uncertain significance (Feb 13, 2024)
3-183492051-G-A		not specified	Uncertain significance (Mar 20, 2024)
3-183492223-C-A		not specified	Uncertain significance (Mar 22, 2023)
3-183492625-T-C		not specified	Uncertain significance (Nov 17, 2022)
3-183494114-C-G		not specified	Uncertain significance (Aug 08, 2023)
3-183494117-C-T		not specified	Uncertain significance (Mar 28, 2024)
3-183494197-C-A		not specified	Uncertain significance (Dec 13, 2023)
3-183494263-T-C		not specified	Uncertain significance (Jun 07, 2024)
3-183499638-A-G		Neoplasm	- (-)
3-183499650-C-T		not specified	Uncertain significance (Jan 23, 2023)
3-183499676-G-A		not specified	Uncertain significance (Dec 01, 2022)
3-183499815-G-T		not specified	Uncertain significance (Jul 08, 2022)
3-183508081-A-C		not specified	Uncertain significance (Jun 29, 2023)
3-183508082-T-C		not specified	Uncertain significance (Jun 13, 2024)
3-183508177-G-A		not specified	Uncertain significance (Oct 17, 2023)
3-183508193-C-T		not specified	Uncertain significance (Jul 12, 2023)
3-183508238-G-A		not specified	Uncertain significance (Feb 23, 2023)
3-183508259-C-G		not specified	Uncertain significance (Dec 09, 2023)
3-183508297-C-T		not specified	Uncertain significance (Mar 01, 2023)
3-183508399-T-G		not specified	Uncertain significance (May 08, 2024)
3-183508493-C-G		not specified	Uncertain significance (Jun 22, 2021)
3-183555386-G-C		Monoclonal B-Cell Lymphocytosis	Uncertain significance (Dec 15, 2015)
3-183555407-A-G		Monoclonal B-Cell Lymphocytosis	Uncertain significance (Dec 15, 2015)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL6	protein_coding	protein_coding	ENST00000341319	7	68159

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000403	0.990	125716	0	32	125748	0.000127

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.24	312	380	0.821	0.0000242	4062
Missense in Polyphen		83	142.37	0.58298		1449
Synonymous	-0.649	176	165	1.06	0.0000117	1205
Loss of Function	2.32	13	25.7	0.506	0.00000128	299

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000276	0.000275
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.0000926	0.0000924
European (Non-Finnish)	0.000176	0.000176
Middle Eastern	0.00	0.00
South Asian	0.000106	0.0000980
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in B-lymphocyte antigen receptor signaling and germinal center formation. {ECO:0000250}.

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.647
• rvis_EVS: -0.91
• rvis_percentile_EVS: 10.07

Haploinsufficiency Scores

• pHI: 0.225
• hipred: Y
• hipred_score: 0.614
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.958

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl6
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: germinal center formation;response to bacterium;B cell receptor signaling pathway
• Molecular function: protein binding