KLHL5

kelch like family member 5, the group of Kelch like|BTB domain containing

Basic information

Region (hg38): 4:39045039-39126857

Links

ENSG00000109790 ∙ NCBI:51088 ∙ OMIM:608064 ∙ HGNC:6356 ∙ Uniprot:Q96PQ7 ∙ 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 KLHL5 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL5 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			28			28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				2		2
non coding						0
Total	0	0	28	0	0

Variants in KLHL5

This is a list of pathogenic ClinVar variants found in the KLHL5 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-39062729-C-T		not specified	Uncertain significance (Feb 26, 2024)
4-39062839-T-G		not specified	Uncertain significance (Aug 18, 2023)
4-39062858-G-A		not specified	Uncertain significance (Apr 09, 2024)
4-39062912-C-A		not specified	Uncertain significance (Jun 09, 2022)
4-39063027-T-A		not specified	Uncertain significance (Dec 14, 2023)
4-39076053-G-A		not specified	Uncertain significance (May 30, 2024)
4-39076096-A-G		not specified	Uncertain significance (Aug 12, 2021)
4-39081192-G-A		not specified	Uncertain significance (Mar 31, 2024)
4-39081223-C-G		not specified	Uncertain significance (May 31, 2023)
4-39081965-C-T		not specified	Uncertain significance (Apr 13, 2023)
4-39081975-T-C		not specified	Uncertain significance (May 27, 2022)
4-39082011-C-T		not specified	Uncertain significance (May 03, 2023)
4-39082137-A-C		not specified	Uncertain significance (Nov 15, 2021)
4-39096740-T-C		not specified	Uncertain significance (Oct 20, 2023)
4-39096755-A-G		not specified	Uncertain significance (Jan 04, 2022)
4-39096813-G-A		not specified	Uncertain significance (Jun 07, 2024)
4-39096833-A-G		not specified	Uncertain significance (Dec 13, 2023)
4-39103317-G-A		not specified	Uncertain significance (Jun 02, 2023)
4-39107601-G-A		not specified	Uncertain significance (Jan 07, 2022)
4-39107662-G-A		not specified	Uncertain significance (Mar 02, 2023)
4-39107687-G-A		not specified	Uncertain significance (Jun 05, 2024)
4-39113015-T-C			Likely benign (Jul 01, 2022)
4-39113020-A-G		not specified	Likely benign (Dec 13, 2023)
4-39113078-G-C		not specified	Uncertain significance (May 24, 2024)
4-39113130-G-A		not specified	Uncertain significance (Jan 29, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL5	protein_coding	protein_coding	ENST00000504108	11	81819

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000528	1.00	125659	0	89	125748	0.000354

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.94	301	412	0.731	0.0000207	4943
Missense in Polyphen		102	172.4	0.59164		2026
Synonymous	0.337	141	146	0.965	0.00000741	1459
Loss of Function	3.15	15	35.2	0.426	0.00000176	429

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000696	0.000693
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.00	0.00
European (Non-Finnish)	0.000521	0.000519
Middle Eastern	0.000272	0.000272
South Asian	0.000197	0.000196
Other	0.000329	0.000326

dbNSFP

Source: dbNSFP

• 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)

Intolerance Scores

• loftool: 0.866
• rvis_EVS: -0.16
• rvis_percentile_EVS: 42.16

Haploinsufficiency Scores

• pHI: 0.618
• hipred: Y
• hipred_score: 0.554
• ghis: 0.565

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.511

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl5

Gene ontology

• Biological process: biological_process;post-translational protein modification
• Cellular component: cytoplasm;cytosol;cytoskeleton
• Molecular function: molecular_function;actin binding