KLHL17

kelch like family member 17, the group of Kelch like|BTB domain containing

Basic information

Region (hg38): 1:960584-965719

Links

ENSG00000187961 ∙ NCBI:339451 ∙ OMIM:619262 ∙ HGNC:24023 ∙ Uniprot:Q6TDP4 ∙ 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 KLHL17 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHL17 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	4	6
missense			59	2		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				2	4	6
Total	0	0	59	6	8

Variants in KLHL17

This is a list of pathogenic ClinVar variants found in the KLHL17 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-960709-G-C		not specified	Uncertain significance (Feb 05, 2024)
1-960725-G-T		not specified	Uncertain significance (Sep 02, 2024)
1-961321-C-A		not specified	Uncertain significance (May 14, 2024)
1-961330-C-T		not specified	Uncertain significance (Mar 04, 2024)
1-961337-C-G		not specified	Uncertain significance (May 01, 2024)
1-961337-C-T		not specified	Uncertain significance (Apr 07, 2022)
1-961369-C-T		not specified	Uncertain significance (Aug 22, 2022)
1-961372-G-A		not specified	Uncertain significance (Jan 26, 2022)
1-961379-A-C		not specified	Uncertain significance (Jun 18, 2021)
1-961383-C-G		not specified	Uncertain significance (Oct 22, 2021)
1-961397-C-G		not specified	Uncertain significance (Apr 28, 2022)
1-961408-T-A		not specified	Uncertain significance (Apr 23, 2024)
1-961411-C-T		not specified	Uncertain significance (Mar 30, 2024)
1-961476-C-G		not specified	Uncertain significance (Aug 15, 2024)
1-961629-A-G			Likely benign (Jul 06, 2018)
1-961636-G-A		not specified	Uncertain significance (Sep 12, 2023)
1-961645-C-A		not specified	Uncertain significance (Jun 28, 2024)
1-961652-A-G		not specified	Uncertain significance (Aug 06, 2024)
1-961678-C-T			Likely benign (Oct 01, 2024)
1-961718-G-T		not specified	Uncertain significance (May 10, 2024)
1-961739-G-A		not specified	Uncertain significance (Jun 18, 2024)
1-961745-G-A		not specified	Uncertain significance (Dec 06, 2022)
1-961753-G-A			Likely benign (May 24, 2018)
1-961846-T-A		not specified	Uncertain significance (Dec 16, 2021)
1-961905-A-G		not specified	Uncertain significance (Dec 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHL17	protein_coding	protein_coding	ENST00000338591	12	5129

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.31e-16	0.0216	125310	0	60	125370	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.571	467	434	1.08	0.0000313	4083
Missense in Polyphen		167	175.58	0.95114		1558
Synonymous	-8.81	360	201	1.79	0.0000163	1359
Loss of Function	0.459	26	28.6	0.907	0.00000165	292

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000234	0.000234
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000218
Finnish	0.00	0.00
European (Non-Finnish)	0.000379	0.000371
Middle Eastern	0.000219	0.000218
South Asian	0.000164	0.000163
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Substrate-recognition component of some cullin-RING- based BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex. The BCR(KLHL17) mediates the ubiquitination and subsequenct degradation of GLUR6. May play a role in the actin-based neuronal function (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0991

Intolerance Scores

• loftool: 0.386
• rvis_EVS: -2.65
• rvis_percentile_EVS: 0.75

Haploinsufficiency Scores

• pHI: 0.0998
• hipred: N
• hipred_score: 0.352
• ghis: 0.642

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.323

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhl17

Gene ontology

• Biological process: brain development;protein ubiquitination;actin cytoskeleton organization
• Cellular component: extracellular space;postsynaptic density;actin cytoskeleton;cell junction;dendrite cytoplasm;neuronal cell body;postsynaptic membrane
• Molecular function: POZ domain binding;protein-containing complex scaffold activity;actin filament binding