SETD9

SET domain containing 9, the group of SET domain containing

Basic information

Region (hg38): 5:56909259-56925532

Previous symbols: [ "C5orf35" ]

Links

ENSG00000155542 ∙ NCBI:133383 ∙ ∙ HGNC:28508 ∙ Uniprot:Q8NE22 ∙ 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 SETD9 gene.

• Inborn genetic diseases (12 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SETD9 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				1		1
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			6	1		7
Total	0	0	11	2	0

Variants in SETD9

This is a list of pathogenic ClinVar variants found in the SETD9 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-56911180-A-G		not specified	Uncertain significance (May 15, 2023)
5-56911191-G-C		not specified	Uncertain significance (Jul 31, 2023)
5-56911234-C-T		not specified	Uncertain significance (Jan 03, 2022)
5-56911313-T-C			Likely benign (Mar 01, 2022)
5-56911368-C-T		not specified	Uncertain significance (Feb 27, 2024)
5-56913115-A-G		not specified	Uncertain significance (Jan 17, 2024)
5-56913899-G-A		not specified	Uncertain significance (Jan 17, 2024)
5-56913987-A-G		not specified	Uncertain significance (Dec 01, 2023)
5-56914893-G-C		not specified	Uncertain significance (Feb 27, 2023)
5-56914938-AACATTGCCT-A		Ependymoma	Uncertain significance (Dec 29, 2017)
5-56916898-G-T		not specified	Uncertain significance (Aug 14, 2023)
5-56923165-T-C		not specified	Uncertain significance (Jul 30, 2023)
5-56923371-C-T		not specified	Uncertain significance (Aug 10, 2021)
5-56923381-G-C		not specified	Uncertain significance (Jun 29, 2022)
5-56923428-A-C		not specified	Uncertain significance (Jun 01, 2023)
5-56923498-C-T		not specified	Uncertain significance (Dec 13, 2023)
5-56923550-T-A		not specified	Uncertain significance (Nov 08, 2022)
5-56923556-C-T		not specified	Likely benign (Jul 12, 2023)
5-56923828-T-C		not specified	Uncertain significance (Jun 02, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SETD9	protein_coding	protein_coding	ENST00000285947	6	16273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000839	0.934	125621	0	127	125748	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.479	140	157	0.892	0.00000767	1931
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000917	0.000913
Ashkenazi Jewish	0.000200	0.000198
East Asian	0.000334	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.000575	0.000571
Middle Eastern	0.000334	0.000326
South Asian	0.00100	0.000980
Other	0.000990	0.000978

dbNSFP

Source: dbNSFP

• Pathway: Histone Modifications;Gene expression (Transcription);Generic Transcription Pathway;RNA Polymerase II Transcription;Regulation of TP53 Activity through Methylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53 (Consensus)

Intolerance Scores

• rvis_EVS: -0.12
• rvis_percentile_EVS: 45.13

Haploinsufficiency Scores

• pHI: 0.231
• hipred: N
• hipred_score: 0.269
• ghis: 0.470

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.114

Gene Damage Prediction

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

Gene ontology

• Biological process: methylation;regulation of signal transduction by p53 class mediator
• Cellular component: nucleoplasm
• Molecular function: lysine N-methyltransferase activity