SETD9

protein-coding

SET domain containing 9, the group of SET domain containing

Gene summary

Predicted to enable lysine N-methyltransferase activity. Predicted to be involved in regulation of signal transduction by p53 class mediator. Located in mitochondrion. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

C5orf35

MANE transcript

NM_153706.4

Inheritance

—

ClinVar variants

U:32B:3

Top phenotype

Ependymoma

gnomAD constraint

pLI —, LoF o/e 0.55

Max pathogenic AF

—

Genomic locus

chr5:56,909,260-56,925,532

External References & Databases

Ensembl (ENSG00000155542)

Transcript & Mutation Effects

hg38 • Region Span ~16.3 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SETD9 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 1

EpendymomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_153706.4. Only rare variants are included.

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				1 clinvar		1
missense			32 clinvar	2 clinvar		34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	32	3	0	35

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 37 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_153706.4	RefSeq	NP_714917.2	6	MANE Select
ENST00000285947.5	Ensembl	ENSP00000285947.2	6	MANE Select
NM_001171990.3	RefSeq	NP_001165461.1	6	Standard
NM_001323018.2	RefSeq	NP_001309947.1	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Histone Modifications
Gene expression (Transcription)
Generic Transcription Pathway
RNA Polymerase II Transcription
Regulation of TP53 Activity through Methylation

Biological Process

methylation
regulation of signal transduction by p53 class mediator

Molecular Function

lysine N-methyltransferase activity

Cellular Component

nucleoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000285947
Coding exons: 6
Length: 16273
Individuals with no LoFs: 125621
Homozygous LoFs: 0
Heterozygous LoFs: 127
Defined: 125748
p: 0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.479	140	157	0.892	0.00000767	1931
Missense (PolyPhen)		44	49.086	0.89639		618
Synonymous	-0.0287	60	59.7	1.00	0.00000307	584
Loss of Function	1.68	9	16.3	0.551	9.03e-7	183

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00074	0.00074	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0.00020	0.00020	rare
East Asian	0.00033	0.00033	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00058	0.00057	rare
South Asian	0.0010	0.00098	notable
Other	0.00099	0.00098	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

RVIS EVS: -0.12
RVIS percentile EVS: 45.13

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.114

Gene Damage Prediction

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