KLHDC9

kelch domain containing 9

Basic information

Region (hg38): 1:161098361-161100346

Links

ENSG00000162755 ∙ NCBI:126823 ∙ OMIM:617375 ∙ HGNC:28489 ∙ Uniprot:Q8NEP7 ∙ 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 KLHDC9 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KLHDC9 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			29	2		31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	2	0

Variants in KLHDC9

This is a list of pathogenic ClinVar variants found in the KLHDC9 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-161098551-C-T		not specified	Uncertain significance (Jun 19, 2024)
1-161098591-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-161098621-C-T		not specified	Uncertain significance (Apr 26, 2023)
1-161098633-G-A		not specified	Uncertain significance (May 02, 2024)
1-161098674-C-G		not specified	Uncertain significance (Feb 23, 2023)
1-161098684-G-A		not specified	Uncertain significance (Apr 12, 2023)
1-161098692-G-A		not specified	Uncertain significance (Jun 13, 2024)
1-161098731-G-C		not specified	Uncertain significance (Dec 19, 2023)
1-161098758-G-T		not specified	Uncertain significance (Dec 15, 2022)
1-161098767-C-G		not specified	Uncertain significance (Nov 09, 2023)
1-161098768-C-A		not specified	Uncertain significance (Sep 26, 2023)
1-161098768-C-T		not specified	Uncertain significance (Dec 12, 2023)
1-161098770-C-T		not specified	Uncertain significance (May 23, 2024)
1-161098771-G-T		not specified	Uncertain significance (Apr 09, 2024)
1-161098773-A-C		not specified	Uncertain significance (Feb 27, 2024)
1-161098785-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-161098800-G-C		not specified	Uncertain significance (Sep 12, 2023)
1-161098903-C-A		not specified	Uncertain significance (Dec 20, 2021)
1-161098968-C-G		not specified	Uncertain significance (Mar 01, 2024)
1-161098974-G-A		not specified	Uncertain significance (Jan 23, 2024)
1-161099019-A-G		not specified	Uncertain significance (Oct 25, 2023)
1-161099043-C-T		not specified	Uncertain significance (Feb 01, 2023)
1-161099380-T-C		not specified	Uncertain significance (Sep 14, 2023)
1-161099604-C-T		not specified	Uncertain significance (Oct 02, 2023)
1-161099617-C-T		not specified	Uncertain significance (Jun 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KLHDC9	protein_coding	protein_coding	ENST00000368011	4	1986

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.02e-9	0.0924	125499	2	247	125748	0.000991

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.704	174	202	0.861	0.0000103	2183
Missense in Polyphen		69	79.221	0.87098		816
Synonymous	0.0374	78	78.4	0.995	0.00000375	760
Loss of Function	0.0702	14	14.3	0.980	8.06e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00539	0.00526
Ashkenazi Jewish	0.00309	0.00308
East Asian	0.000223	0.000217
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.000837	0.000827
Middle Eastern	0.000223	0.000217
South Asian	0.000653	0.000653
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0873

Intolerance Scores

• loftool: 0.733
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.57

Haploinsufficiency Scores

• pHI: 0.120
• hipred: N
• hipred_score: 0.178
• ghis: 0.426

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.699

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Klhdc9

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component
• Molecular function: cyclin binding