SERTAD2

SERTA domain containing 2

Basic information

Region (hg38): 2:64631621-64751005

Links

ENSG00000179833 ∙ NCBI:9792 ∙ OMIM:617851 ∙ HGNC:30784 ∙ Uniprot:Q14140 ∙ 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 SERTAD2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SERTAD2 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			25	3		28
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	25	4	0

Variants in SERTAD2

This is a list of pathogenic ClinVar variants found in the SERTAD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-64635995-G-A		not specified	Uncertain significance (May 05, 2023)
2-64636043-C-T		not specified	Uncertain significance (Sep 14, 2022)
2-64636070-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-64636073-T-C		not specified	Uncertain significance (Oct 26, 2021)
2-64636114-G-A		not specified	Uncertain significance (Dec 01, 2023)
2-64636168-G-A		not specified	Uncertain significance (May 16, 2023)
2-64636173-C-T			Likely benign (May 01, 2022)
2-64636174-G-A		not specified	Uncertain significance (Apr 19, 2024)
2-64636174-G-C		not specified	Uncertain significance (Aug 26, 2022)
2-64636226-C-T		not specified	Likely benign (May 08, 2023)
2-64636228-C-T		not specified	Uncertain significance (Jun 26, 2023)
2-64636247-C-T		not specified	Uncertain significance (May 04, 2022)
2-64636303-G-A		not specified	Uncertain significance (Dec 14, 2021)
2-64636322-T-G		not specified	Uncertain significance (May 13, 2022)
2-64636327-G-T		not specified	Uncertain significance (Apr 25, 2022)
2-64636414-G-T		not specified	Uncertain significance (Aug 16, 2022)
2-64636415-C-A		not specified	Uncertain significance (Aug 16, 2022)
2-64636417-G-A		not specified	Uncertain significance (Sep 14, 2021)
2-64636447-G-A		not specified	Uncertain significance (Jul 14, 2021)
2-64636457-C-T		not specified	Uncertain significance (Sep 01, 2021)
2-64636514-G-A		not specified	Uncertain significance (Dec 16, 2023)
2-64636534-G-A		not specified	Uncertain significance (Apr 15, 2024)
2-64636540-G-A		not specified	Uncertain significance (Jan 10, 2023)
2-64636589-C-T		not specified	Uncertain significance (Jun 10, 2024)
2-64636614-G-T		not specified	Uncertain significance (Jul 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SERTAD2	protein_coding	protein_coding	ENST00000313349	1	119385

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.881	0.118	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.676	165	191	0.862	0.0000118	2056
Missense in Polyphen		35	67.513	0.51842		790
Synonymous	-1.04	102	89.5	1.14	0.00000681	663
Loss of Function	2.44	0	6.93	0.00	3.82e-7	89

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts at E2F-responsive promoters as coregulator to integrate signals provided by PHD- and/or bromodomain-containing transcription factors. May act as coactivator as well as corepressor of E2F1-TFDP1 and E2F4-TFDP1 complexes on E2F consensus binding sites, which would activate or inhibit E2F- target genes expression. Modulates fat storage by down-regulating the expression of key genes involved in adipocyte lipolysis, thermogenesis and oxidative metabolism. {ECO:0000269|PubMed:11331592}.
• Pathway: Glucocorticoid Receptor Pathway;Nuclear Receptors Meta-Pathway (Consensus)

Recessive Scores

• pRec: 0.0961

Intolerance Scores

• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.41

Haploinsufficiency Scores

• pHI: 0.790
• hipred: Y
• hipred_score: 0.599
• ghis: 0.554

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0899

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sertad2
• Phenotype: immune system phenotype; liver/biliary system phenotype; hematopoietic system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); cellular phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype

Gene ontology

• Biological process: negative regulation of cell growth;positive regulation of transcription, DNA-templated
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol
• Molecular function: transcription coactivator activity