KLHL30

protein-coding

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

Gene summary

Predicted to enable ubiquitin-like ligase-substrate adaptor activity. Predicted to be involved in proteasome-mediated ubiquitin-dependent protein catabolic process. Predicted to be part of Cul3-RING ubiquitin ligase complex. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_198582.4

Inheritance

—

ClinVar variants

U:130B:10

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.82

Max pathogenic AF

—

Genomic locus

chr2:238,138,668-238,152,947

External References & Databases

Ensembl (ENSG00000168427)

Transcript & Mutation Effects

hg38 • Region Span ~14.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to KLHL30 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 137

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_198582.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				1 clinvar		1
missense			129 clinvar	9 clinvar		138
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	130	10	0	140

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 9 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_198582.4	RefSeq	NP_940984.3	7	MANE Select
ENST00000409223.2	Ensembl	ENSP00000386389.1	7	MANE Select
ENST00000964871.1	Ensembl	ENSP00000634930.1	6	Standard
ENST00000964871.2	Ensembl	ENSP00000634930.1	6	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000409223
Coding exons: 7
Length: 14226
Individuals with no LoFs: 124455
Homozygous LoFs: 0
Heterozygous LoFs: 111
Defined: 124566
p: 0.000446

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.507	334	361	0.925	0.0000251	3610
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00069	0.00058	rare
Latino/Admixed American	0.00031	0.00029	rare
Ashkenazi Jewish	0.0053	0.0052	notable
East Asian	0.00023	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00029	0.00027	rare
South Asian	0.00017	0.00016	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.782
RVIS EVS: -0.26
RVIS percentile EVS: 34.93

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.464

Gene Damage Prediction

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