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.

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.

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				2	2	4
missense			41	2	1	44
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					1	1
Total	0	0	41	4	4

Variants in KLHL1

This is a list of pathogenic ClinVar variants found in the KLHL1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-69701716-T-C		not specified	Uncertain significance (Jul 06, 2021)
13-69707667-G-T		not specified	Uncertain significance (Nov 08, 2022)
13-69707668-T-C		not specified	Uncertain significance (Jun 24, 2022)
13-69707678-T-C			Uncertain significance (May 01, 2022)
13-69707729-C-A		not specified	Uncertain significance (Feb 15, 2023)
13-69707752-C-T		not specified	Uncertain significance (Jun 02, 2023)
13-69707762-C-A		not specified	Uncertain significance (Dec 17, 2023)
13-69707771-T-C		not specified	Uncertain significance (Sep 06, 2022)
13-69719390-C-T		not specified	Uncertain significance (Apr 07, 2022)
13-69719445-C-T		not specified	Uncertain significance (May 17, 2023)
13-69719450-C-T		not specified	Uncertain significance (Feb 13, 2024)
13-69719490-G-A		not specified	Uncertain significance (Mar 18, 2024)
13-69719493-C-T		not specified	Uncertain significance (Aug 12, 2021)
13-69740514-T-C		not specified	Uncertain significance (Oct 06, 2022)
13-69740531-A-C		not specified	Uncertain significance (Sep 15, 2021)
13-69796904-C-T		not specified	Uncertain significance (Dec 27, 2023)
13-69838986-A-T		not specified	Uncertain significance (Dec 15, 2023)
13-69839032-G-A		not specified	Uncertain significance (Dec 22, 2023)
13-69839078-G-C		not specified	Uncertain significance (May 14, 2024)
13-69882324-T-C		not specified	Uncertain significance (May 04, 2022)
13-69882370-C-A		not specified	Uncertain significance (Apr 20, 2024)
13-69882383-A-T		not specified	Uncertain significance (Jan 30, 2024)
13-69882407-T-C		not specified	Uncertain significance (Feb 13, 2024)
13-69882420-T-C		not specified	Uncertain significance (Nov 17, 2022)
13-69940045-T-C		not specified	Uncertain significance (Aug 10, 2021)

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