KLHDC1

kelch domain containing 1

Basic information

Region (hg38): 14:49693105-49753150

Links

ENSG00000197776NCBI:122773OMIM:611281HGNC:19836Uniprot:Q8N7A1AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the KLHDC1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC1 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
26
clinvar
26
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 26 0 0

Variants in KLHDC1

This is a list of pathogenic ClinVar variants found in the KLHDC1 region.

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

Position Type Phenotype Significance ClinVar
14-49693203-C-G not specified Uncertain significance (Jul 27, 2024)3534901
14-49693240-C-T not specified Uncertain significance (Feb 13, 2024)3115361
14-49693247-C-T not specified Uncertain significance (Oct 04, 2022)2269830
14-49693249-G-A not specified Uncertain significance (Sep 26, 2024)3534906
14-49693277-G-T not specified Uncertain significance (Jul 26, 2021)2408826
14-49693279-G-C not specified Uncertain significance (Sep 20, 2023)3115364
14-49693279-G-T not specified Uncertain significance (Jul 07, 2022)2299979
14-49709160-C-T not specified Uncertain significance (Jun 22, 2021)2234136
14-49709168-G-C not specified Uncertain significance (Aug 10, 2021)2221474
14-49709748-G-A not specified Uncertain significance (Dec 10, 2024)3534898
14-49709768-G-C not specified Uncertain significance (Jun 07, 2023)2570256
14-49710291-A-G not specified Uncertain significance (Mar 18, 2024)3288843
14-49710300-A-G not specified Uncertain significance (Nov 24, 2024)2380482
14-49710303-T-G not specified Uncertain significance (Feb 05, 2024)3115359
14-49710347-C-A not specified Uncertain significance (Aug 28, 2024)3534902
14-49710348-G-A not specified Uncertain significance (Jan 11, 2023)2468932
14-49710359-T-C not specified Uncertain significance (Oct 22, 2021)2215485
14-49710363-G-C not specified Uncertain significance (Aug 02, 2022)2305001
14-49723930-T-C not specified Uncertain significance (Jun 24, 2022)2297629
14-49723935-G-A not specified Uncertain significance (Dec 22, 2023)3115360
14-49725687-A-G not specified Uncertain significance (Nov 08, 2024)3534907
14-49728926-G-A not specified Uncertain significance (Sep 14, 2022)2385995
14-49728953-G-A not specified Uncertain significance (Nov 20, 2024)3534899
14-49728960-C-T not specified Uncertain significance (Dec 13, 2023)3115362
14-49728961-A-A Benign (Jul 10, 2017)776837

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KLHDC1protein_codingprotein_codingENST00000359332 1360048
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
4.48e-80.9521256881581257470.000235
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3971892050.9220.000009922675
Missense in Polyphen6874.1860.91662901
Synonymous0.9005867.40.8610.00000329682
Loss of Function1.961627.00.5930.00000135322

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0003430.000342
Ashkenazi Jewish0.000.00
East Asian0.0001830.000163
Finnish0.000.00
European (Non-Finnish)0.0003470.000316
Middle Eastern0.0001830.000163
South Asian0.0003350.000327
Other0.0003660.000326

dbNSFP

Source: dbNSFP

Recessive Scores

pRec
0.105

Intolerance Scores

loftool
rvis_EVS
-0.51
rvis_percentile_EVS
21.41

Haploinsufficiency Scores

pHI
0.550
hipred
N
hipred_score
0.426
ghis
0.605

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.225

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Klhdc1
Phenotype

Gene ontology

Biological process
Cellular component
cytosol
Molecular function