KLHDC10

kelch domain containing 10

Basic information

Region (hg38): 7:130070534-130135705

Links

ENSG00000128607 ∙ NCBI:23008 ∙ OMIM:615152 ∙ HGNC:22194 ∙ Uniprot:Q6PID8 ∙ 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 KLHDC10 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC10 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						0
Total	0	0	9	0	0

Variants in KLHDC10

This is a list of pathogenic ClinVar variants found in the KLHDC10 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-130070728-G-C		not specified	Uncertain significance (Dec 16, 2021)
7-130096933-T-G		not specified	Uncertain significance (Feb 12, 2024)
7-130096956-C-T		not specified	Uncertain significance (Dec 19, 2023)
7-130116628-C-T		not specified	Uncertain significance (Sep 17, 2021)
7-130120788-C-T		not specified	Uncertain significance (Apr 20, 2023)
7-130120871-C-T		not specified	Uncertain significance (Oct 26, 2022)
7-130120887-G-A		not specified	Uncertain significance (May 12, 2024)
7-130124522-A-T		not specified	Uncertain significance (Jan 17, 2024)
7-130129470-T-C		not specified	Uncertain significance (Apr 09, 2024)
7-130129508-T-C		not specified	Uncertain significance (Jul 06, 2021)
7-130130589-G-A		not specified	Uncertain significance (Jul 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC10	protein_coding	protein_coding	ENST00000335420	10	65211

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.926	0.0744	125736	0	6	125742	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.41	90	238	0.378	0.0000127	2858
Missense in Polyphen		19	84.658	0.22443		916
Synonymous	0.490	81	86.8	0.933	0.00000459	876
Loss of Function	3.99	4	25.9	0.154	0.00000166	269

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
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	0.0000328	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Participates in the oxidative stress-induced cell death through MAP3K5 activation. Inhibits PPP5C phosphatase activity on MAP3K5. {ECO:0000269|PubMed:23102700}.

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.205
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.783
• ghis: 0.593

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.987

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhdc10

Gene ontology

• Biological process: positive regulation of stress-activated MAPK cascade
• Cellular component: nucleoplasm;cytoplasm
• Molecular function: protein binding