KLHL23

kelch like family member 23, the group of Kelch like|BTB domain containing

Basic information

Region (hg38): 2:169694488-169776989

Links

ENSG00000213160 ∙ NCBI:151230 ∙ ∙ HGNC:27506 ∙ Uniprot:Q8NBE8 ∙ 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 KLHL23 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL23 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						0
missense			17	1	1	19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	1	1

Variants in KLHL23

This is a list of pathogenic ClinVar variants found in the KLHL23 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-169700976-A-G		not specified	Uncertain significance (Dec 14, 2021)
2-169701008-A-G		not specified	Uncertain significance (Apr 04, 2023)
2-169701021-A-G		not specified	Uncertain significance (Mar 24, 2023)
2-169701195-C-A		not specified	Uncertain significance (Aug 10, 2021)
2-169701203-A-G		not specified	Uncertain significance (Mar 06, 2023)
2-169701266-G-T		not specified	Uncertain significance (Jan 26, 2023)
2-169701276-C-T		not specified	Uncertain significance (Apr 22, 2022)
2-169701309-G-A		not specified	Likely benign (Nov 15, 2021)
2-169701461-C-G		not specified	Uncertain significance (Jun 27, 2022)
2-169701501-T-C		not specified	Uncertain significance (Jun 06, 2023)
2-169701682-T-G		not specified	Uncertain significance (Nov 17, 2022)
2-169701686-A-G		not specified	Uncertain significance (Mar 22, 2023)
2-169735063-A-G		not specified	Likely benign (Nov 18, 2022)
2-169735084-G-A		not specified	Uncertain significance (Jun 17, 2024)
2-169735172-C-T		not specified	Uncertain significance (Oct 04, 2022)
2-169735174-G-A		not specified	Uncertain significance (Dec 27, 2023)
2-169735445-C-G		not specified	Uncertain significance (May 31, 2024)
2-169735570-A-G		not specified	Uncertain significance (Feb 05, 2024)
2-169735661-T-C		not specified	Uncertain significance (May 21, 2024)
2-169735664-A-G		not specified	Uncertain significance (Apr 08, 2022)
2-169735741-A-G		not specified	Uncertain significance (Sep 20, 2023)
2-169735805-A-G			Benign (Mar 30, 2018)
2-169735812-G-T		not specified	Uncertain significance (Sep 29, 2023)
2-169735895-C-A		not specified	Uncertain significance (Mar 18, 2024)
2-169735901-C-T		not specified	Uncertain significance (Jan 05, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL23	protein_coding	protein_coding	ENST00000392647	3	82502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00416	0.994	125721	0	26	125747	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.733	262	298	0.880	0.0000144	3688
Missense in Polyphen		70	111.64	0.62702		1370
Synonymous	0.143	106	108	0.982	0.00000575	1025
Loss of Function	2.79	8	22.2	0.361	0.00000116	290

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000123	0.000120
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000278	0.000272
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000975	0.0000967
Middle Eastern	0.000278	0.000272
South Asian	0.000174	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.123

Intolerance Scores

• loftool: 0.647
• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.252
• hipred: N
• hipred_score: 0.454
• ghis: 0.543

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.773

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl23

Gene ontology

• Molecular function: protein binding