SUPT20H

SPT20 homolog, SAGA complex component, the group of SAGA complex

Basic information

Region (hg38): 13:37009311-37059713

Previous symbols: [ "C13orf19", "FAM48A" ]

Links

ENSG00000102710 ∙ NCBI:55578 ∙ OMIM:613417 ∙ HGNC:20596 ∙ Uniprot:Q8NEM7 ∙ 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 SUPT20H gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUPT20H 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			30			30
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	0

Variants in SUPT20H

This is a list of pathogenic ClinVar variants found in the SUPT20H region.

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

Position	Type	Phenotype	Significance	ClinVar
13-37009778-A-G		not specified	Uncertain significance (Jul 07, 2022)
13-37010595-A-C		not specified	Uncertain significance (Aug 30, 2021)
13-37017297-G-C		not specified	Uncertain significance (May 24, 2023)
13-37021517-C-T		not specified	Uncertain significance (Oct 12, 2022)
13-37022023-A-G		not specified	Uncertain significance (Apr 18, 2023)
13-37022030-T-G		not specified	Uncertain significance (May 15, 2024)
13-37022033-T-A		not specified	Uncertain significance (Jun 29, 2023)
13-37024092-G-T		not specified	Uncertain significance (Jan 26, 2022)
13-37024128-T-C		not specified	Uncertain significance (Dec 20, 2021)
13-37024162-G-T		not specified	Uncertain significance (Aug 23, 2021)
13-37024424-C-T		not specified	Uncertain significance (Mar 04, 2024)
13-37025355-T-G		not specified	Uncertain significance (Aug 21, 2023)
13-37026214-C-T		not specified	Uncertain significance (Sep 25, 2023)
13-37026225-C-A		not specified	Uncertain significance (May 08, 2023)
13-37028172-C-T		not specified	Uncertain significance (May 26, 2024)
13-37028187-T-C		not specified	Uncertain significance (Feb 27, 2023)
13-37028190-C-T		not specified	Uncertain significance (Dec 22, 2023)
13-37028191-A-G		not specified	Uncertain significance (Oct 17, 2023)
13-37028227-G-T		not specified	Uncertain significance (Jan 23, 2023)
13-37031574-T-G		not specified	Uncertain significance (Jul 25, 2023)
13-37031623-A-G		not specified	Uncertain significance (Jun 24, 2022)
13-37031747-C-A		not specified	Uncertain significance (Mar 04, 2024)
13-37033456-T-C		not specified	Uncertain significance (Jan 23, 2024)
13-37033507-A-T		not specified	Uncertain significance (Oct 06, 2021)
13-37033573-G-A		not specified	Uncertain significance (Apr 12, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUPT20H	protein_coding	protein_coding	ENST00000350612	25	50402

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-14	0.992	125690	0	58	125748	0.000231

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.18	325	391	0.832	0.0000193	5031
Missense in Polyphen		53	75.86	0.69865		1021
Synonymous	0.651	126	136	0.929	0.00000676	1479
Loss of Function	2.66	30	50.3	0.596	0.00000236	631

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000381	0.000381
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.000321	0.000316
Middle Eastern	0.000381	0.000381
South Asian	0.000201	0.000163
Other	0.000176	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for MAP kinase p38 (MAPK11, MAPK12, MAPK13 and/or MAPK14) activation during gastrulation. Required for down- regulation of E-cadherin during gastrulation by regulating E- cadherin protein level downstream from NCK-interacting kinase (NIK) and independently of the regulation of transcription by FGF signaling and Snail (By similarity). Required for starvation- induced ATG9A trafficking during autophagy. {ECO:0000250, ECO:0000269|PubMed:19893488}.
• Pathway: Autophagy - animal - Homo sapiens (human);Chromatin modifying enzymes;HATs acetylate histones;Chromatin organization (Consensus)

Recessive Scores

• pRec: 0.123

Intolerance Scores

• rvis_EVS: -0.44
• rvis_percentile_EVS: 24.46

Haploinsufficiency Scores

• pHI: 0.513
• hipred: Y
• hipred_score: 0.552
• ghis: 0.607

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: K

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Supt20
• Phenotype: growth/size/body region phenotype; vision/eye 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); 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); pigmentation phenotype; embryo 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)

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;autophagy;gastrulation;positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter
• Cellular component: SAGA complex;fibrillar center;SAGA-type complex
• Molecular function: transcription coregulator activity;protein binding