SETD7

SET domain containing 7, histone lysine methyltransferase, the group of SET domain containing|Lysine methyltransferases

Basic information

Region (hg38): 4:139495940-139606699

Links

ENSG00000145391 ∙ NCBI:80854 ∙ OMIM:606594 ∙ HGNC:30412 ∙ Uniprot:Q8WTS6 ∙ 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 SETD7 gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SETD7 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						0
Total	0	0	5	0	1

Variants in SETD7

This is a list of pathogenic ClinVar variants found in the SETD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-139517889-C-T		not specified	Uncertain significance (Jun 28, 2022)
4-139517893-G-C		not specified	Uncertain significance (Nov 08, 2022)
4-139517897-C-G		not specified	Uncertain significance (Dec 09, 2023)
4-139517942-C-G		not specified	Uncertain significance (Sep 07, 2022)
4-139523369-G-A		not specified	Uncertain significance (Jan 03, 2022)
4-139533194-G-A		not specified	Uncertain significance (May 16, 2022)
4-139533320-C-T		not specified	Uncertain significance (Dec 08, 2023)
4-139547024-C-T			Benign (Dec 31, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SETD7	protein_coding	protein_coding	ENST00000274031	8	110759

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00423	0.989	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.66	143	211	0.679	0.0000112	2403
Missense in Polyphen		46	76.362	0.60239		812
Synonymous	-0.229	85	82.4	1.03	0.00000506	687
Loss of Function	2.38	7	17.8	0.393	8.12e-7	229

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000322	0.0000322
Ashkenazi Jewish	0.00169	0.00169
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000973	0.0000967
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone methyltransferase that specifically monomethylates 'Lys-4' of histone H3. H3 'Lys-4' methylation represents a specific tag for epigenetic transcriptional activation. Plays a central role in the transcriptional activation of genes such as collagenase or insulin. Recruited by IPF1/PDX-1 to the insulin promoter, leading to activate transcription. Has also methyltransferase activity toward non-histone proteins such as p53/TP53, TAF10, and possibly TAF7 by recognizing and binding the [KR]-[STA]-K in substrate proteins. Monomethylates 'Lys-189' of TAF10, leading to increase the affinity of TAF10 for RNA polymerase II. Monomethylates 'Lys-372' of p53/TP53, stabilizing p53/TP53 and increasing p53/TP53-mediated transcriptional activation. {ECO:0000269|PubMed:12540855, ECO:0000269|PubMed:12588998, ECO:0000269|PubMed:15099517, ECO:0000269|PubMed:15525938, ECO:0000269|PubMed:16141209, ECO:0000269|PubMed:17108971}.
• Pathway: Lysine degradation - Homo sapiens (human);FoxO signaling pathway - Homo sapiens (human);Carnitine Synthesis;Histone Modifications;PKMTs methylate histone lysines;Chromatin modifying enzymes;Lysine metabolism;Chromatin organization;p53 pathway (Consensus)

Recessive Scores

• pRec: 0.156

Intolerance Scores

• loftool: 0.273
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.578
• hipred: Y
• hipred_score: 0.831
• ghis: 0.498

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: Setd7
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; immune system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype

Zebrafish Information Network

• Gene name: setd7
• Affected structure: heart
• Phenotype tag: abnormal
• Phenotype quality: linear

Gene ontology

• Biological process: chromatin organization;cellular response to DNA damage stimulus;peptidyl-lysine monomethylation;peptidyl-lysine dimethylation;histone lysine methylation;response to ethanol;positive regulation of transcription, DNA-templated;regulation of histone H3-K9 methylation;heterochromatin organization
• Cellular component: nucleoplasm;chromosome;nucleolus
• Molecular function: p53 binding;chromatin binding;protein binding;protein-lysine N-methyltransferase activity;histone-lysine N-methyltransferase activity