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.

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.

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			20			20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	20	0	0

Variants in SUGT1

This is a list of pathogenic ClinVar variants found in the SUGT1 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-52652925-C-T		not specified	Uncertain significance (Jul 25, 2024)
13-52652946-C-T		not specified	Uncertain significance (Oct 29, 2024)
13-52653046-G-A		not specified	Likely benign (Nov 13, 2024)
13-52653052-C-A		not specified	Uncertain significance (Sep 12, 2024)
13-52653055-G-C		not specified	Uncertain significance (Dec 28, 2022)
13-52653074-A-C		not specified	Uncertain significance (Nov 03, 2022)
13-52653083-G-A		not specified	Uncertain significance (Jun 21, 2021)
13-52653093-C-T		not specified	Uncertain significance (Jul 03, 2024)
13-52657539-C-T		not specified	Uncertain significance (Aug 02, 2022)
13-52657604-C-G		not specified	Uncertain significance (Jan 24, 2025)
13-52658456-T-C		not specified	Uncertain significance (Apr 06, 2023)
13-52659193-A-C		not specified	Uncertain significance (Jan 20, 2025)
13-52661547-A-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
13-52662682-G-C		not specified	Uncertain significance (Feb 03, 2025)
13-52662688-A-T		not specified	Uncertain significance (Jan 24, 2023)
13-52663110-G-T		not specified	Uncertain significance (May 02, 2024)
13-52665682-G-C		not specified	Uncertain significance (Aug 05, 2024)
13-52665707-G-C		not specified	Uncertain significance (Jan 19, 2024)
13-52676232-T-G		not specified	Uncertain significance (Oct 19, 2024)
13-52679980-A-G		not specified	Uncertain significance (Jan 16, 2024)
13-52680057-A-T		not specified	Uncertain significance (Jan 03, 2025)
13-52680124-A-T		not specified	Uncertain significance (May 08, 2023)
13-52687765-A-G		not specified	Uncertain significance (Mar 21, 2023)
13-52687770-T-A		not specified	Uncertain significance (Mar 19, 2024)
13-52687803-C-A		not specified	Uncertain significance (Jan 27, 2025)

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