KLHDC9

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			58 clinvar	2 clinvar		60
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	61	5	0	66

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_152366.5	RefSeq	NP_689579.3	4	MANE Select
ENST00000368011.9	Ensembl	ENSP00000356990.4	4	MANE Select
NM_001007255.3	RefSeq	NP_001007256.1	3	Standard
ENST00000392192.6	Ensembl	ENSP00000376030.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process

Molecular Function

cyclin binding

Cellular Component

cellular_component

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368011
Coding exons: 4
Length: 1986
Individuals with no LoFs: 125499
Homozygous LoFs: 2
Heterozygous LoFs: 247
Defined: 125748
p: 0.000991

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.704	174	202	0.861	0.0000103	2183
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0047	0.0046	notable
Latino/Admixed American	0.00064	0.00064	rare
Ashkenazi Jewish	0.0031	0.0031	notable
East Asian	0.00022	0.00022	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00084	0.00083	rare
South Asian	0.00065	0.00065	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0873

Intolerance Scores

LoFtool: 0.733
RVIS EVS: 0.75
RVIS percentile EVS: 86.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.699

Gene Damage Prediction

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