KLHL21

kelch like family member 21, the group of Kelch like|BTB domain containing

Basic information

Region (hg38): 1:6590724-6614607

Links

ENSG00000162413 ∙ NCBI:9903 ∙ OMIM:616262 ∙ HGNC:29041 ∙ Uniprot:Q9UJP4 ∙ 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 KLHL21 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL21 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	2	7
missense			35	3	1	39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	37	8	3

Variants in KLHL21

This is a list of pathogenic ClinVar variants found in the KLHL21 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-6593380-G-A		KLHL21-related disorder	Benign (Mar 06, 2020)
1-6593388-G-A		not specified	Uncertain significance (May 24, 2023)
1-6593390-G-A		not specified	Likely benign (Apr 12, 2023)
1-6593396-C-T		not specified	Uncertain significance (Feb 21, 2024)
1-6593402-C-G		not specified	Uncertain significance (Nov 26, 2024)
1-6593447-C-T		not specified	Uncertain significance (Jul 26, 2021)
1-6593456-G-A		not specified	Likely benign (Dec 03, 2024)
1-6593459-A-G		not specified	Uncertain significance (Jul 19, 2023)
1-6593460-A-T		not specified	Uncertain significance (Jul 19, 2023)
1-6593462-G-A		not specified	Uncertain significance (Oct 28, 2024)
1-6593523-G-A		not specified	Uncertain significance (Sep 10, 2024)
1-6593537-C-A		not specified	Uncertain significance (Mar 14, 2023)
1-6593579-G-A		not specified	Uncertain significance (Dec 28, 2023)
1-6593627-C-A		not specified	Uncertain significance (Apr 04, 2023)
1-6595498-G-A		not specified	Uncertain significance (Apr 01, 2024)
1-6599090-C-T		not specified	Uncertain significance (Sep 14, 2022)
1-6599110-T-C		not specified	Uncertain significance (Apr 09, 2024)
1-6599176-T-C		not specified	Uncertain significance (May 31, 2023)
1-6599232-G-A		KLHL21-related disorder	Likely benign (Jul 11, 2019)
1-6599233-T-C		not specified	Uncertain significance (Dec 03, 2024)
1-6599242-G-A		not specified	Uncertain significance (May 05, 2023)
1-6599284-T-C		not specified	Uncertain significance (Jun 24, 2022)
1-6599291-A-T		not specified	Uncertain significance (Sep 23, 2023)
1-6599297-C-T		not specified	Uncertain significance (Oct 24, 2024)
1-6599306-C-T		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL21	protein_coding	protein_coding	ENST00000377658	4	23884

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.31e-7	0.699	125704	0	15	125719	0.0000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.49	266	344	0.774	0.0000206	3755
Missense in Polyphen		52	97.464	0.53353		1123
Synonymous	-3.57	218	160	1.36	0.0000106	1264
Loss of Function	1.17	12	17.2	0.696	7.46e-7	187

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000841	0.0000791
Middle Eastern	0.0000544	0.0000544
South Asian	0.000132	0.000131
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-specific adapter of a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex required for efficient chromosome alignment and cytokinesis. The BCR(KLHL21) E3 ubiquitin ligase complex regulates localization of the chromosomal passenger complex (CPC) from chromosomes to the spindle midzone in anaphase and mediates the ubiquitination of AURKB. Ubiquitination of AURKB by BCR(KLHL21) E3 ubiquitin ligase complex may not lead to its degradation by the proteasome. {ECO:0000269|PubMed:14528312, ECO:0000269|PubMed:19995937}.
• 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: 0.117

Haploinsufficiency Scores

• pHI: 0.285
• hipred: Y
• hipred_score: 0.813
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.887

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl21
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: cell cycle;protein ubiquitination;regulation of cytokinesis;chromosome passenger complex localization to spindle midzone;post-translational protein modification;cell division
• Cellular component: polar microtubule;cytosol;Cul3-RING ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity