KLHL4

kelch like family member 4, the group of BTB domain containing|Kelch like

Basic information

Region (hg38): X:87517409-87670050

Links

ENSG00000102271 ∙ NCBI:56062 ∙ OMIM:300348 ∙ HGNC:6355 ∙ Uniprot:Q9C0H6 ∙ 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 KLHL4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL4 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				3		3
missense			19			19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	3	0

Variants in KLHL4

This is a list of pathogenic ClinVar variants found in the KLHL4 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-87517913-A-C		not specified	Uncertain significance (Mar 20, 2024)
X-87518015-A-G		not specified	Uncertain significance (Sep 06, 2022)
X-87518029-A-T		not specified	Uncertain significance (May 16, 2024)
X-87518104-C-A		not specified	Uncertain significance (Aug 17, 2021)
X-87518198-C-G		not specified	Uncertain significance (Aug 02, 2022)
X-87518228-A-T		not specified	Uncertain significance (Jun 27, 2022)
X-87518236-T-G		not specified	Uncertain significance (May 23, 2023)
X-87518260-C-G		not specified	Uncertain significance (Mar 25, 2022)
X-87613893-T-G		not specified	Uncertain significance (Apr 13, 2022)
X-87613933-A-G		not specified	Uncertain significance (Aug 01, 2022)
X-87613946-C-T			Likely benign (Jun 18, 2018)
X-87614505-A-T		not specified	Uncertain significance (Mar 01, 2023)
X-87618073-T-C		not specified	Uncertain significance (Mar 22, 2022)
X-87622365-G-A		not specified	Uncertain significance (Jul 26, 2022)
X-87625694-C-A		not specified	Uncertain significance (Dec 22, 2023)
X-87632226-A-G			Likely benign (Sep 01, 2022)
X-87632386-A-G		not specified	Uncertain significance (Oct 10, 2023)
X-87632404-C-T		not specified	Uncertain significance (Mar 26, 2024)
X-87632417-C-T		not specified	Uncertain significance (Dec 21, 2022)
X-87632425-C-T		not specified	Uncertain significance (Oct 25, 2022)
X-87633803-G-C		not specified	Uncertain significance (Apr 05, 2023)
X-87633870-A-T			Likely benign (Nov 01, 2022)
X-87633908-A-G		not specified	Uncertain significance (Dec 30, 2023)
X-87635573-A-G		not specified	Uncertain significance (Mar 03, 2022)
X-87635660-T-A		not specified	Uncertain significance (Oct 05, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL4	protein_coding	protein_coding	ENST00000373114	11	152299

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.663	0.337	125594	3	3	125600	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.892	220	261	0.845	0.0000187	4732
Missense in Polyphen		82	106.8	0.76776		1954
Synonymous	-0.898	103	92.0	1.12	0.00000665	1384
Loss of Function	3.44	4	21.0	0.191	0.00000152	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000400	0.0000400
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000246	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000158	0.0000653
Other	0.000222	0.000163

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0858

Intolerance Scores

• loftool: 0.240
• rvis_EVS: -0.36
• rvis_percentile_EVS: 28.93

Haploinsufficiency Scores

• pHI: 0.409
• hipred: Y
• hipred_score: 0.531
• ghis: 0.450

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0747

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl4

Gene ontology

• Biological process: biological_process
• Cellular component: cytoplasm;microtubule organizing center;microtubule cytoskeleton
• Molecular function: molecular_function;actin binding