SUGT1

SGT1 homolog, MIS12 kinetochore complex assembly cochaperone

Basic information

Region (hg38): 13:52652709-52700909

Links

ENSG00000165416

∙ NCBI:10910 ∙ OMIM:604098 ∙ HGNC:16987 ∙ Uniprot:Q9Y2Z0 ∙ 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 SUGT1 gene.

not_specified (32 variants)
EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SUGT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000006704.5. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				2 clinvar		2
missense			30 clinvar			30
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	30	2	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SUGT1	protein_coding	protein_coding	ENST00000343788	14	48201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.453	0.547	125737	0	10	125747	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.00	134	171	0.785	0.00000791	2385
Missense in Polyphen		24	44.808	0.53562		626
Synonymous	-0.263	63	60.4	1.04	0.00000302	639
Loss of Function	3.49	5	23.1	0.217	9.76e-7	318

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)	0.0000630	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000136	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: May play a role in ubiquitination and subsequent proteasomal degradation of target proteins.;
Pathway: NOD-like receptor signaling pathway - Homo sapiens (human);Nucleotide-binding Oligomerization Domain (NOD) pathway;The NLRP3 inflammasome;Inflammasomes;Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways;Innate Immune System;Immune System (Consensus)

Recessive Scores

pRec: 0.0952

Intolerance Scores

loftool: 0.778
rvis_EVS: -0.18
rvis_percentile_EVS: 39.95

Haploinsufficiency Scores

pHI: 0.250
hipred: Y
hipred_score: 0.827
ghis: 0.620

Essentials

essential_gene_CRISPR: E
essential_gene_CRISPR2: E
essential_gene_gene_trap: E
gene_indispensability_pred: E
gene_indispensability_score: 0.797

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Sugt1
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);

Gene ontology

Biological process: mitotic cell cycle;regulation of protein stability;positive regulation by host of symbiont catalytic activity;protein stabilization
Cellular component: ubiquitin ligase complex;kinetochore;nucleus;cytosol;protein-containing complex
Molecular function: protein binding