SUGT1

protein-coding

SGT1 homolog, MIS12 kinetochore complex assembly cochaperone

Gene summary

This gene encodes a highly conserved nuclear protein involved in kinetochore function and required for the G1/S and G2/M transitions. This protein interacts with heat shock protein 90. Alternative splicing results in multiple transcript variants. Pseudogenes for this gene have been defined on several different chromosomes. [provided by RefSeq, Mar 2016]

MANE transcript

NM_006704.5

Inheritance

—

ClinVar variants

U:42B:3

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.22

Max pathogenic AF

—

Genomic locus

chr13:52,652,709-52,700,909

External References & Databases

Ensembl (ENSG00000165416)

Transcript & Mutation Effects

hg38 • Region Span ~48.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SUGT1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 35

not providedTotal: 2

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006704.5. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar	3 clinvar		4
missense			36 clinvar			36
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	0	0	42	3	0	45

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 47 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006704.5	RefSeq	NP_006695.1	13	MANE Select
ENST00000310528.9	Ensembl	ENSP00000308067.7	13	MANE Select
NM_001130912.3	RefSeq	NP_001124384.1	14	Standard
NM_001320831.2	RefSeq	NP_001307760.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

mitotic cell cycle
regulation of protein stability
positive regulation by host of symbiont catalytic activity
protein stabilization

Molecular Function

protein binding

Cellular Component

ubiquitin ligase complex
kinetochore
nucleus
cytosol
protein-containing complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000343788
Coding exons: 14
Length: 48201
Individuals with no LoFs: 125737
Homozygous LoFs: 0
Heterozygous LoFs: 10
Defined: 125747
p: 0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.00	134	171	0.785	0.00000791	2385
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.000063	0.000062	rare
South Asian	0.00014	0.000098	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a role in ubiquitination and subsequent proteasomal degradation of target proteins.;

Recessive Scores

pRec: 0.0952

Intolerance Scores

LoFtool: 0.778
RVIS EVS: -0.18
RVIS percentile EVS: 39.95

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.797

Gene Damage Prediction

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