KLHL1

kelch like family member 1, the group of Kelch like|BTB domain containing

Basic information

Region (hg38): 13:69700594-70108493

Links

ENSG00000150361 ∙ NCBI:57626 ∙ OMIM:605332 ∙ HGNC:6352 ∙ Uniprot:Q9NR64 ∙ 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 KLHL1 gene.

• not_specified (100 variants)
• not_provided (5 variants)
• KLHL1-related_disorder (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000020866.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				2	1	3
missense			100	2		102
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	100	4	1

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL1	protein_coding	protein_coding	ENST00000377844	11	407866

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.19e-7	0.999	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0797	392	396	0.989	0.0000184	4887
Missense in Polyphen		111	146.96	0.75532		1810
Synonymous	-1.26	165	146	1.13	0.00000714	1454
Loss of Function	2.89	16	34.3	0.467	0.00000166	415

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000300
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000169	0.000167
Middle Eastern	0.00	0.00
South Asian	0.000169	0.000163
Other	0.000167	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in organizing the actin cytoskeleton of the brain cells.

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.417
• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.53

Haploinsufficiency Scores

• pHI: 0.209
• hipred: Y
• hipred_score: 0.604
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.342

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: adult walking behavior;dendrite development;cerebellar Purkinje cell layer development;actin cytoskeleton organization
• Cellular component: cytoplasm;cytoskeleton;dendrite;neuronal cell body
• Molecular function: actin binding