SETD4

SET domain containing 4, the group of SET domain containing

Basic information

Region (hg38): 21:36034540-36079389

Previous symbols: [ "C21orf27", "C21orf18" ]

Links

ENSG00000185917 ∙ NCBI:54093 ∙ ∙ HGNC:1258 ∙ Uniprot:Q9NVD3 ∙ 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 SETD4 gene.

• Inborn genetic diseases (30 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SETD4 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						0
missense			12	4		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			15	1	1	17
Total	0	0	27	5	1

Variants in SETD4

This is a list of pathogenic ClinVar variants found in the SETD4 region.

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

Position	Type	Phenotype	Significance	ClinVar
21-36036152-C-T		not specified	Likely benign (May 26, 2023)
21-36036228-T-A			Likely benign (Mar 01, 2022)
21-36036232-T-G		not specified	Uncertain significance (Aug 12, 2021)
21-36040611-G-C		not specified	Uncertain significance (Jun 29, 2022)
21-36043793-T-C		not specified	Uncertain significance (Jul 14, 2023)
21-36043847-C-T		not specified	Uncertain significance (Sep 14, 2021)
21-36043862-G-C		not specified	Uncertain significance (Nov 14, 2023)
21-36043866-C-T		not specified	Uncertain significance (Dec 19, 2023)
21-36043901-C-T		not specified	Uncertain significance (Oct 04, 2022)
21-36043910-G-A		not specified	Uncertain significance (Aug 30, 2021)
21-36043918-T-A		not specified	Uncertain significance (Nov 09, 2021)
21-36043920-C-T		not specified	Uncertain significance (Sep 13, 2023)
21-36043946-G-A		not specified	Uncertain significance (Dec 09, 2023)
21-36045589-T-C		not specified	Likely benign (Apr 25, 2022)
21-36045619-G-A		not specified	Uncertain significance (Aug 03, 2022)
21-36045623-C-T		not specified	Uncertain significance (Oct 22, 2021)
21-36045626-G-A		not specified	Uncertain significance (Jun 11, 2021)
21-36045800-A-G		not specified	Uncertain significance (Jan 03, 2024)
21-36045940-C-T		not specified	Likely benign (Mar 29, 2022)
21-36045974-T-C		not specified	Uncertain significance (Nov 08, 2022)
21-36046001-G-A		not specified	Uncertain significance (Nov 14, 2023)
21-36057126-G-A		not specified	Uncertain significance (Jan 10, 2022)
21-36070239-C-G		not specified	Uncertain significance (Sep 12, 2023)
21-36070261-A-G		not specified	Uncertain significance (Feb 21, 2024)
21-36070270-C-T		not specified	Uncertain significance (Jun 06, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SETD4	protein_coding	protein_coding	ENST00000399215	10	44849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.04e-13	0.0902	125589	0	159	125748	0.000632

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.344	221	236	0.937	0.0000130	2843
Missense in Polyphen		63	70.287	0.89633		862
Synonymous	0.759	88	97.5	0.902	0.00000624	848
Loss of Function	0.616	21	24.3	0.865	0.00000128	283

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00124	0.00123
Ashkenazi Jewish	0.00377	0.00378
East Asian	0.000652	0.000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000354	0.000352
Middle Eastern	0.000652	0.000544
South Asian	0.00101	0.00101
Other	0.000652	0.000652

dbNSFP

Source: dbNSFP

• Pathway: Histone Modifications;Metabolism of lipids;Synthesis of Prostaglandins (PG) and Thromboxanes (TX);Prostaglandin Leukotriene metabolism;Arachidonic acid metabolism;Leukotriene metabolism;Metabolism;Fatty acid metabolism;Prostaglandin formation from arachidonate;Prostaglandin formation from dihomo gama-linoleic acid;Putative anti-Inflammatory metabolites formation from EPA;Arachidonic acid metabolism (Consensus)

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.742
• rvis_EVS: -0.18
• rvis_percentile_EVS: 40.36

Haploinsufficiency Scores

• pHI: 0.134
• hipred: N
• hipred_score: 0.233
• ghis: 0.558

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.520

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Setd4
• Phenotype: pigmentation phenotype; vision/eye phenotype

Gene ontology

• Biological process: peptidyl-lysine trimethylation;peptidyl-lysine monomethylation
• Molecular function: protein-lysine N-methyltransferase activity