SUPT7L

SPT7 like, STAGA complex subunit gamma, the group of SAGA complex

Basic information

Region (hg38): 2:27650808-27663840

Links

ENSG00000119760 ∙ NCBI:9913 ∙ OMIM:612762 ∙ HGNC:30632 ∙ Uniprot:O94864 ∙ 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 SUPT7L gene.

• Inborn genetic diseases (21 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUPT7L 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			21			21
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	21	0	0

Variants in SUPT7L

This is a list of pathogenic ClinVar variants found in the SUPT7L region.

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

Position	Type	Phenotype	Significance	ClinVar
2-27653546-C-G		not specified	Uncertain significance (Jul 12, 2023)
2-27653564-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-27653616-T-C		not specified	Uncertain significance (Jan 23, 2023)
2-27653667-A-C		not specified	Uncertain significance (Jul 27, 2022)
2-27653678-T-C		not specified	Uncertain significance (May 03, 2023)
2-27655403-G-A		not specified	Uncertain significance (Mar 06, 2023)
2-27655454-C-T		not specified	Uncertain significance (Jun 17, 2022)
2-27655488-C-T		not specified	Uncertain significance (Aug 02, 2023)
2-27655540-G-C		not specified	Uncertain significance (Dec 22, 2023)
2-27657426-A-T		not specified	Uncertain significance (Dec 01, 2022)
2-27657440-C-G		not specified	Uncertain significance (Dec 01, 2022)
2-27657441-C-T		not specified	Uncertain significance (Jan 06, 2023)
2-27657467-C-T		not specified	Uncertain significance (Jun 21, 2022)
2-27657481-C-T		not specified	Uncertain significance (Jun 16, 2023)
2-27657565-T-A		not specified	Uncertain significance (Apr 26, 2023)
2-27657598-G-A		not specified	Uncertain significance (May 24, 2023)
2-27657598-G-C		not specified	Uncertain significance (Nov 29, 2021)
2-27657625-C-T		not specified	Uncertain significance (Apr 22, 2022)
2-27657631-G-C		not specified	Uncertain significance (Jun 12, 2023)
2-27661014-C-T		not specified	Uncertain significance (Jan 23, 2023)
2-27661048-C-T		not specified	Uncertain significance (Feb 27, 2024)
2-27661173-C-T		not specified	Uncertain significance (Mar 17, 2023)
2-27661210-G-A		not specified	Uncertain significance (Oct 06, 2021)
2-27661327-G-T		not specified	Uncertain significance (Jan 31, 2024)
2-27661356-T-G		not specified	Uncertain significance (Jan 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUPT7L	protein_coding	protein_coding	ENST00000337768	5	12998

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0485	0.947	124771	0	33	124804	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.943	200	241	0.829	0.0000134	2739
Missense in Polyphen		49	62.725	0.78119		644
Synonymous	0.525	80	86.2	0.928	0.00000447	814
Loss of Function	2.50	5	15.7	0.319	7.51e-7	186

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000316	0.000316
Ashkenazi Jewish	0.000211	0.000199
East Asian	0.000167	0.000167
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.000133	0.000132
Middle Eastern	0.000167	0.000167
South Asian	0.000168	0.000163
Other	0.000165	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization;C-MYC pathway;Validated targets of C-MYC transcriptional activation (Consensus)

Recessive Scores

• pRec: 0.288

Intolerance Scores

• rvis_EVS: -0.14
• rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

• pHI: 0.130
• hipred: Y
• hipred_score: 0.783
• ghis: 0.601

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K
• gene_indispensability_pred: E
• gene_indispensability_score: 0.956

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Supt7l
• Phenotype: homeostasis/metabolism phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); growth/size/body region 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)

Gene ontology

• Biological process: histone H3 acetylation;maintenance of protein location in nucleus;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;STAGA complex
• Molecular function: transcription coactivator activity;histone acetyltransferase activity;protein binding;protein heterodimerization activity