KLHL30

kelch like family member 30, the group of BTB domain containing|Kelch like

Basic information

Region (hg38): 2:238138668-238152947

Links

ENSG00000168427 ∙ NCBI:377007 ∙ ∙ HGNC:24770 ∙ Uniprot:Q0D2K2 ∙ 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 KLHL30 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL30 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				1		1
missense			83	6		89
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	83	7	0

Variants in KLHL30

This is a list of pathogenic ClinVar variants found in the KLHL30 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-238140762-G-A		not specified	Uncertain significance (Sep 01, 2021)
2-238140767-G-A		not specified	Uncertain significance (Apr 22, 2022)
2-238140772-T-A		not specified	Uncertain significance (Aug 17, 2021)
2-238140857-G-T		not specified	Uncertain significance (Feb 28, 2023)
2-238140875-G-A		not specified	Uncertain significance (Nov 20, 2024)
2-238140896-C-T		not specified	Uncertain significance (Mar 29, 2023)
2-238140953-G-A		not specified	Uncertain significance (Dec 06, 2022)
2-238140956-G-A		not specified	Uncertain significance (Jun 29, 2023)
2-238140969-C-T		not specified	Uncertain significance (Apr 09, 2024)
2-238140972-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-238140983-C-A			Likely benign (Jul 01, 2022)
2-238140984-G-A		not specified	Uncertain significance (Sep 03, 2024)
2-238140998-G-A		not specified	Uncertain significance (Aug 28, 2024)
2-238141001-G-A		not specified	Uncertain significance (Dec 14, 2023)
2-238141014-T-C		not specified	Uncertain significance (Dec 14, 2021)
2-238141022-T-G		not specified	Uncertain significance (Jan 31, 2022)
2-238141050-C-T		not specified	Uncertain significance (Jul 06, 2021)
2-238141076-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-238141121-G-A		not specified	Uncertain significance (Aug 10, 2021)
2-238141124-C-T		not specified	Uncertain significance (Jan 23, 2024)
2-238141125-G-A		not specified	Uncertain significance (Jun 28, 2024)
2-238141151-G-A		not specified	Likely benign (Mar 14, 2023)
2-238141178-G-A		not specified	Uncertain significance (Oct 06, 2021)
2-238141191-G-T		not specified	Uncertain significance (Dec 14, 2021)
2-238141193-C-A		not specified	Uncertain significance (Nov 20, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL30	protein_coding	protein_coding	ENST00000409223	7	14226

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.45e-11	0.214	124455	0	111	124566	0.000446

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.507	334	361	0.925	0.0000251	3610
Missense in Polyphen		116	132.03	0.87857		1352
Synonymous	0.522	169	178	0.950	0.0000138	1219
Loss of Function	0.764	18	21.9	0.824	0.00000118	234

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000998	0.000883
Ashkenazi Jewish	0.00529	0.00519
East Asian	0.000227	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000286	0.000275
Middle Eastern	0.000227	0.000223
South Asian	0.000166	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.782
• rvis_EVS: -0.26
• rvis_percentile_EVS: 34.93

Haploinsufficiency Scores

• pHI: 0.0783
• hipred: N
• hipred_score: 0.251
• ghis: 0.514

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.464

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl30
• Phenotype: skeleton phenotype