SETD3

SET domain containing 3, actin histidine methyltransferase, the group of SET domain containing

Basic information

Region (hg38): 14:99397748-99480889

Previous symbols: [ "C14orf154" ]

Links

ENSG00000183576 ∙ NCBI:84193 ∙ OMIM:615671 ∙ HGNC:20493 ∙ Uniprot:Q86TU7 ∙ 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 SETD3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SETD3 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					4	4
missense			48	3		51
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	48	3	4

Variants in SETD3

This is a list of pathogenic ClinVar variants found in the SETD3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-99398699-T-C		not specified	Likely benign (Dec 13, 2021)
14-99398773-C-G		not specified	Uncertain significance (Feb 21, 2024)
14-99398779-C-T		not specified	Uncertain significance (Oct 20, 2023)
14-99398825-C-T		not specified	Uncertain significance (Nov 09, 2021)
14-99398848-C-T		not specified	Uncertain significance (Feb 08, 2025)
14-99398869-A-G		not specified	Uncertain significance (Oct 12, 2021)
14-99398870-C-T		not specified	Uncertain significance (Mar 08, 2025)
14-99398896-A-G		not specified	Uncertain significance (Apr 12, 2024)
14-99398909-G-A		not specified	Uncertain significance (Nov 26, 2024)
14-99398915-A-T		not specified	Uncertain significance (Jul 15, 2021)
14-99398930-T-C		not specified	Likely benign (Mar 16, 2022)
14-99398959-T-A		not specified	Uncertain significance (Nov 21, 2024)
14-99398985-C-T		not specified	Uncertain significance (Feb 22, 2024)
14-99398995-C-T		not specified	Uncertain significance (Dec 20, 2021)
14-99398996-G-A		not specified	Uncertain significance (Oct 06, 2021)
14-99398998-T-C		not specified	Uncertain significance (Jan 19, 2025)
14-99399009-G-T		not specified	Uncertain significance (Jan 21, 2025)
14-99399025-T-G		not specified	Uncertain significance (Feb 14, 2023)
14-99399062-G-A		not specified	Uncertain significance (Dec 19, 2023)
14-99399079-T-G		not specified	Likely benign (Jun 29, 2023)
14-99399085-C-T		not specified	Uncertain significance (Nov 12, 2024)
14-99399113-C-T		not specified	Uncertain significance (Jan 23, 2023)
14-99400110-T-C		not specified	Uncertain significance (Jun 28, 2022)
14-99400192-T-G		not specified	Uncertain significance (Sep 26, 2024)
14-99400227-C-T		not specified	Uncertain significance (Dec 22, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SETD3	protein_coding	protein_coding	ENST00000331768	12	83134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0208	0.979	125722	0	26	125748	0.000103

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.45	260	335	0.776	0.0000192	3908
Missense in Polyphen		36	79.185	0.45463		890
Synonymous	-0.823	140	128	1.09	0.00000821	1119
Loss of Function	3.66	9	30.9	0.291	0.00000187	335

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.000163	0.000163
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.000163	0.000163
South Asian	0.000164	0.000163
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Histone methyltransferase that methylates 'Lys-4' and 'Lys-36' of histone H3 (H3K4me and H3K36me). Acts as a transcriptional activator. Plays an important role in the transcriptional regulation of muscle cell differentiation via interaction with MYOD1. {ECO:0000250|UniProtKB:Q91WC0}.
• Pathway: Lysine degradation - Homo sapiens (human);Histone Modifications;PKMTs methylate histone lysines;Chromatin modifying enzymes;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.416
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.55

Haploinsufficiency Scores

• pHI: 0.294
• hipred: Y
• hipred_score: 0.738
• ghis: 0.602

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.290

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Setd3
• Phenotype: limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; growth/size/body region phenotype

Gene ontology

• Biological process: histone H3-K36 methylation;peptidyl-lysine trimethylation;peptidyl-lysine monomethylation;peptidyl-lysine dimethylation;positive regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of muscle cell differentiation;histone H3-K4 methylation
• Cellular component: nuclear chromatin;nucleoplasm
• Molecular function: RNA polymerase II activating transcription factor binding;transcription coactivator activity;protein-lysine N-methyltransferase activity;histone-lysine N-methyltransferase activity;histone methyltransferase activity (H3-K4 specific);histone methyltransferase activity (H3-K36 specific)