KLHL42

kelch like family member 42, the group of Kelch like

Basic information

Region (hg38): 12:27780048-27803040

Previous symbols: [ "KLHDC5" ]

Links

ENSG00000087448 ∙ NCBI:57542 ∙ OMIM:618919 ∙ HGNC:29252 ∙ Uniprot:Q9P2K6 ∙ 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 KLHL42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL42 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			11			11
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	0	0

Variants in KLHL42

This is a list of pathogenic ClinVar variants found in the KLHL42 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-27780370-C-G		not specified	Uncertain significance (Nov 09, 2023)
12-27780470-G-A		not specified	Uncertain significance (Jul 13, 2022)
12-27780739-G-T		not specified	Uncertain significance (Aug 17, 2021)
12-27780751-G-T		not specified	Uncertain significance (Jan 08, 2024)
12-27780854-C-T		not specified	Uncertain significance (Feb 17, 2024)
12-27780908-C-T		not specified	Uncertain significance (Apr 12, 2024)
12-27780919-G-T		not specified	Uncertain significance (Feb 05, 2024)
12-27781093-C-G		not specified	Uncertain significance (Jun 16, 2023)
12-27781142-C-T		not specified	Uncertain significance (Oct 02, 2023)
12-27791800-A-G		not specified	Uncertain significance (Nov 03, 2022)
12-27791821-C-A		not specified	Uncertain significance (Dec 16, 2023)
12-27791830-A-C		not specified	Uncertain significance (Mar 06, 2023)
12-27791873-T-G		not specified	Uncertain significance (Apr 15, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL42	protein_coding	protein_coding	ENST00000381271	3	23021

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0125	0.981	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	217	291	0.746	0.0000156	3260
Missense in Polyphen		73	104.4	0.69924		1202
Synonymous	0.0597	131	132	0.993	0.00000776	1039
Loss of Function	2.37	6	16.3	0.367	7.84e-7	179

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.0000994	0.0000992
East Asian	0.000109	0.000109
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

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(KLHL42) E3 ubiquitin ligase complex mediates the ubiquitination and subsequent degradation of KATNA1. Involved in microtubule dynamics throughout mitosis. {ECO:0000269|PubMed:19261606}.
• 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)

Recessive Scores

• pRec: 0.109

Intolerance Scores

• rvis_EVS: -0.47
• rvis_percentile_EVS: 23.04

Haploinsufficiency Scores

• pHI: 0.228
• hipred: Y
• hipred_score: 0.673
• ghis: 0.625

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl42

Zebrafish Information Network

• Gene name: klhl42
• Affected structure: pancreatic B cell
• Phenotype tag: abnormal
• Phenotype quality: decreased area

Gene ontology

• Biological process: protein polyubiquitination;cell cycle;regulation of microtubule-based process;proteasome-mediated ubiquitin-dependent protein catabolic process;post-translational protein modification;cell division
• Cellular component: spindle;cytosol;Cul3-RING ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding