KLHL38

kelch like family member 38, the group of BTB domain containing|Kelch like

Basic information

Region (hg38): 8:123644442-123653801

Links

ENSG00000175946 ∙ NCBI:340359 ∙ ∙ HGNC:34435 ∙ Uniprot:Q2WGJ6 ∙ 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 KLHL38 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL38 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
missense			55	1	2	58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	55	1	4

Variants in KLHL38

This is a list of pathogenic ClinVar variants found in the KLHL38 region.

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

Position	Type	Phenotype	Significance	ClinVar
8-123645759-G-A		not specified	Uncertain significance (Feb 17, 2022)
8-123645864-C-T		not specified	Uncertain significance (Feb 27, 2023)
8-123645870-C-T		not specified	Uncertain significance (Dec 21, 2023)
8-123645887-G-A		not specified	Uncertain significance (Jun 18, 2024)
8-123645896-C-T		not specified	Uncertain significance (May 17, 2023)
8-123645897-G-A		not specified	Uncertain significance (Oct 26, 2021)
8-123645912-C-T		not specified	Uncertain significance (May 10, 2022)
8-123645953-C-A		not specified	Uncertain significance (Jun 03, 2024)
8-123645999-G-T		not specified	Uncertain significance (Mar 22, 2023)
8-123646927-G-A		not specified	Uncertain significance (May 23, 2023)
8-123646967-C-A		not specified	Uncertain significance (Jun 18, 2024)
8-123646981-T-G		not specified	Uncertain significance (Jun 29, 2023)
8-123651594-G-A		not specified	Uncertain significance (Aug 02, 2023)
8-123651617-C-T		not specified	Uncertain significance (May 09, 2024)
8-123651627-A-G		not specified	Uncertain significance (Jun 06, 2022)
8-123651640-T-A		not specified	Uncertain significance (Oct 10, 2023)
8-123651648-C-A		not specified	Uncertain significance (Mar 27, 2023)
8-123651648-C-T		not specified	Uncertain significance (Nov 09, 2023)
8-123651691-C-A		not specified	Uncertain significance (Sep 14, 2022)
8-123651705-A-G		not specified	Uncertain significance (Sep 17, 2021)
8-123651709-G-T		not specified	Uncertain significance (Oct 06, 2021)
8-123651732-C-T		not specified	Uncertain significance (Jul 06, 2022)
8-123651741-C-G		not specified	Uncertain significance (Jun 29, 2023)
8-123651747-C-G			Benign (Aug 23, 2019)
8-123651755-A-G		not specified	Uncertain significance (Nov 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL38	protein_coding	protein_coding	ENST00000325995	3	7424

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.41e-8	0.374	124715	1	96	124812	0.000389

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-1.23	412	348	1.19	0.0000206	3827
Missense in Polyphen		95	80.444	1.1809		820
Synonymous	-2.28	185	149	1.24	0.00000992	1139
Loss of Function	0.791	14	17.6	0.796	8.32e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000598	0.000597
Ashkenazi Jewish	0.00	0.00
East Asian	0.000612	0.000612
Finnish	0.00	0.00
European (Non-Finnish)	0.000487	0.000477
Middle Eastern	0.000612	0.000612
South Asian	0.000687	0.000654
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.442
• rvis_EVS: 0.52
• rvis_percentile_EVS: 80.37

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.251
• ghis: 0.447

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.202

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl38

Gene ontology

• Molecular function: protein binding