KLHL29

kelch like family member 29, the group of BTB domain containing|Kelch like

Basic information

Region (hg38): 2:23385178-23708611

Previous symbols: [ "KBTBD9" ]

Links

ENSG00000119771 ∙ NCBI:114818 ∙ ∙ HGNC:29404 ∙ Uniprot:Q96CT2 ∙ 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 KLHL29 gene.

• Inborn genetic diseases (42 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL29 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				1		1
missense			40	1		41
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	40	2	0

Variants in KLHL29

This is a list of pathogenic ClinVar variants found in the KLHL29 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-23562204-G-A		not specified	Uncertain significance (Dec 21, 2022)
2-23562221-G-A		not specified	Uncertain significance (Jan 17, 2023)
2-23562234-G-A		not specified	Uncertain significance (Nov 02, 2021)
2-23562263-G-A		not specified	Uncertain significance (Oct 04, 2022)
2-23562279-G-A		not specified	Uncertain significance (Jul 08, 2022)
2-23562288-G-A		not specified	Uncertain significance (Jan 26, 2022)
2-23562309-G-C		not specified	Uncertain significance (Jan 04, 2024)
2-23562314-G-A		not specified	Uncertain significance (Dec 22, 2023)
2-23562321-G-T		not specified	Uncertain significance (Nov 03, 2023)
2-23562341-G-A		not specified	Uncertain significance (Jul 25, 2023)
2-23562353-C-T		not specified	Uncertain significance (May 22, 2023)
2-23562381-G-A		not specified	Uncertain significance (Jun 28, 2022)
2-23562422-G-A		not specified	Uncertain significance (Jan 16, 2024)
2-23562431-G-A		not specified	Uncertain significance (Sep 16, 2022)
2-23562477-C-A		not specified	Uncertain significance (Jan 23, 2023)
2-23639193-C-T		not specified	Uncertain significance (Dec 15, 2022)
2-23639206-C-T		not specified	Uncertain significance (Aug 18, 2023)
2-23639243-G-C		not specified	Uncertain significance (Dec 21, 2023)
2-23639261-G-A		not specified	Uncertain significance (Feb 15, 2023)
2-23642406-G-A		not specified	Uncertain significance (Nov 18, 2022)
2-23642415-C-A		not specified	Uncertain significance (Jun 06, 2023)
2-23642431-C-A		not specified	Uncertain significance (Sep 28, 2022)
2-23642503-C-T		not specified	Uncertain significance (Dec 19, 2022)
2-23642536-C-T		not specified	Uncertain significance (May 31, 2023)
2-23642562-G-A		not specified	Uncertain significance (Jul 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL29	protein_coding	protein_coding	ENST00000486442	12	323394

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.985	0.0147	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.40	302	520	0.581	0.0000345	5624
Missense in Polyphen		77	184.54	0.41726		1957
Synonymous	1.96	200	238	0.839	0.0000186	1826
Loss of Function	4.44	4	30.4	0.131	0.00000144	369

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• rvis_EVS: -0.54
• rvis_percentile_EVS: 20.54

Haploinsufficiency Scores

• pHI: 0.745
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl29
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); muscle phenotype; hearing/vestibular/ear 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)