KLHL17

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

Basic information

Region (hg38): 1:960584-965719

Links

ENSG00000187961NCBI:339451OMIM:619262HGNC:24023Uniprot:Q6TDP4AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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
clinvar
4
clinvar
6
missense
59
clinvar
2
clinvar
61
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
1
1
non coding
2
clinvar
4
clinvar
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)3115507
1-961321-C-A not specified Uncertain significance (May 14, 2024)3288912
1-961330-C-T not specified Uncertain significance (Mar 04, 2024)3115502
1-961337-C-G not specified Uncertain significance (May 01, 2024)3288901
1-961337-C-T not specified Uncertain significance (Apr 07, 2022)2378213
1-961369-C-T not specified Uncertain significance (Aug 22, 2022)2308800
1-961372-G-A not specified Uncertain significance (Jan 26, 2022)2273289
1-961379-A-C not specified Uncertain significance (Jun 18, 2021)2230643
1-961383-C-G not specified Uncertain significance (Oct 22, 2021)2256501
1-961397-C-G not specified Uncertain significance (Apr 28, 2022)2286750
1-961408-T-A not specified Uncertain significance (Apr 23, 2024)3288911
1-961411-C-T not specified Uncertain significance (Mar 30, 2024)3288908
1-961629-A-G Likely benign (Jul 06, 2018)782832
1-961636-G-A not specified Uncertain significance (Sep 12, 2023)2622406
1-961678-C-T Likely benign (Oct 01, 2024)3388534
1-961718-G-T not specified Uncertain significance (May 10, 2024)3288900
1-961739-G-A not specified Uncertain significance (Jun 18, 2024)3288905
1-961745-G-A not specified Uncertain significance (Dec 06, 2022)2333582
1-961753-G-A Likely benign (May 24, 2018)714060
1-961846-T-A not specified Uncertain significance (Dec 16, 2021)2267574
1-961905-A-G not specified Uncertain significance (Dec 30, 2023)2384970
1-961973-G-A not specified Uncertain significance (Feb 23, 2023)2469111
1-961985-G-T not specified Uncertain significance (Mar 14, 2023)2495893
1-962018-G-A not specified Uncertain significance (May 20, 2024)3288903
1-962346-C-T Benign (Jul 23, 2018)784924

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KLHL17protein_codingprotein_codingENST00000338591 125129
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.31e-160.02161253100601253700.000239
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.5714674341.080.00003134083
Missense in Polyphen167175.580.951141558
Synonymous-8.813602011.790.00001631359
Loss of Function0.4592628.60.9070.00000165292

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002340.000234
Ashkenazi Jewish0.000.00
East Asian0.0002190.000218
Finnish0.000.00
European (Non-Finnish)0.0003790.000371
Middle Eastern0.0002190.000218
South Asian0.0001640.000163
Other0.0001640.000163

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Klhl17
Phenotype

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