KLHDC3

kelch domain containing 3

Basic information

Region (hg38): 6:43014102-43021298

Links

ENSG00000124702 ∙ NCBI:116138 ∙ OMIM:611248 ∙ HGNC:20704 ∙ Uniprot:Q9BQ90 ∙ 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 KLHDC3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC3 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1		2
Total	0	0	10	1	0

Variants in KLHDC3

This is a list of pathogenic ClinVar variants found in the KLHDC3 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-43017200-G-A		not specified	Uncertain significance (Mar 29, 2023)
6-43017256-G-A		not specified	Uncertain significance (May 24, 2024)
6-43017316-C-T		not specified	Uncertain significance (Jul 25, 2023)
6-43017322-A-G		not specified	Uncertain significance (May 22, 2023)
6-43017548-G-A		not specified	Uncertain significance (Dec 21, 2023)
6-43017551-A-C		not specified	Uncertain significance (Oct 31, 2022)
6-43017557-G-A		not specified	Uncertain significance (Dec 28, 2023)
6-43017622-C-T			Likely benign (Sep 01, 2022)
6-43017662-G-T		not specified	Uncertain significance (Feb 27, 2024)
6-43017856-C-T		not specified	Uncertain significance (Oct 25, 2023)
6-43018206-T-C		not specified	Uncertain significance (May 16, 2024)
6-43019115-G-A		not specified	Uncertain significance (Mar 16, 2024)
6-43019324-T-C		not specified	Uncertain significance (Jul 13, 2022)
6-43020699-A-G		not specified	Uncertain significance (Jan 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC3	protein_coding	protein_coding	ENST00000326974	10	7086

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.999	0.000924	125746	0	2	125748	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.45	93	245	0.380	0.0000160	2510
Missense in Polyphen		18	110.12	0.16346		1057
Synonymous	0.637	83	90.7	0.915	0.00000549	751
Loss of Function	4.17	0	20.2	0.00	0.00000102	225

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000879	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in meiotic recombination process.
• Pathway: XBP1(S) activates chaperone genes (Consensus)

Recessive Scores

• pRec: 0.273

Intolerance Scores

• rvis_EVS: -0.38
• rvis_percentile_EVS: 27.42

Haploinsufficiency Scores

• pHI: 0.382
• hipred: Y
• hipred_score: 0.728
• ghis: 0.652

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.900

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhdc3

Gene ontology

• Biological process: reciprocal meiotic recombination;IRE1-mediated unfolded protein response
• Cellular component: nuclear chromatin;nucleoplasm;cytoplasm;cytosol
• Molecular function: chromatin binding;protein binding