KLHDC1

kelch domain containing 1

Basic information

Region (hg38): 14:49693105-49753150

Links

ENSG00000197776 ∙ NCBI:122773 ∙ OMIM:611281 ∙ HGNC:19836 ∙ Uniprot:Q8N7A1 ∙ 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 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			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)
14-49693240-C-T		not specified	Uncertain significance (Feb 13, 2024)
14-49693247-C-T		not specified	Uncertain significance (Oct 04, 2022)
14-49693249-G-A		not specified	Uncertain significance (Sep 26, 2024)
14-49693277-G-T		not specified	Uncertain significance (Jul 26, 2021)
14-49693279-G-C		not specified	Uncertain significance (Sep 20, 2023)
14-49693279-G-T		not specified	Uncertain significance (Jul 07, 2022)
14-49709160-C-T		not specified	Uncertain significance (Jun 22, 2021)
14-49709168-G-C		not specified	Uncertain significance (Aug 10, 2021)
14-49709748-G-A		not specified	Uncertain significance (Dec 10, 2024)
14-49709768-G-C		not specified	Uncertain significance (Jun 07, 2023)
14-49710291-A-G		not specified	Uncertain significance (Mar 18, 2024)
14-49710300-A-G		not specified	Uncertain significance (Nov 24, 2024)
14-49710303-T-G		not specified	Uncertain significance (Feb 05, 2024)
14-49710347-C-A		not specified	Uncertain significance (Aug 28, 2024)
14-49710348-G-A		not specified	Uncertain significance (Jan 11, 2023)
14-49710359-T-C		not specified	Uncertain significance (Oct 22, 2021)
14-49710363-G-C		not specified	Uncertain significance (Aug 02, 2022)
14-49723930-T-C		not specified	Uncertain significance (Jun 24, 2022)
14-49723935-G-A		not specified	Uncertain significance (Dec 22, 2023)
14-49725687-A-G		not specified	Uncertain significance (Nov 08, 2024)
14-49728926-G-A		not specified	Uncertain significance (Sep 14, 2022)
14-49728953-G-A		not specified	Uncertain significance (Nov 20, 2024)
14-49728960-C-T		not specified	Uncertain significance (Dec 13, 2023)
14-49728961-A-A			Benign (Jul 10, 2017)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC1	protein_coding	protein_coding	ENST00000359332	13	60048

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.48e-8	0.952	125688	1	58	125747	0.000235

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	189	205	0.922	0.00000992	2675
Missense in Polyphen		68	74.186	0.91662		901
Synonymous	0.900	58	67.4	0.861	0.00000329	682
Loss of Function	1.96	16	27.0	0.593	0.00000135	322

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000343	0.000342
Ashkenazi Jewish	0.00	0.00
East Asian	0.000183	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000347	0.000316
Middle Eastern	0.000183	0.000163
South Asian	0.000335	0.000327
Other	0.000366	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.105

Intolerance Scores

• 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

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

Mouse Genome Informatics

• Gene name: Klhdc1

Gene ontology

• Cellular component: cytosol