SAGE1

protein-coding

sarcoma antigen 1, the group of SAGE family

Gene summary

This gene belongs to a class of genes that are activated in tumors. These genes are expressed in tumors of different histologic types but not in normal tissues, except for spermatogenic cells and, for some, placenta. The proteins encoded by these genes appear to be strictly tumor specific, and hence may be excellent sources of antigens for cancer immunotherapy. This gene is expressed in sarcomas. [provided by RefSeq, Jul 2008]

MANE transcript

NM_001381902.1

Inheritance

—

ClinVar variants

U:101B:38

Top phenotype

SAGE1-related disorder

gnomAD constraint

pLI —, LoF o/e 0.95

Max pathogenic AF

—

Genomic locus

chrX:135,890,182-135,913,062

External References & Databases

Ensembl (ENSG00000181433)

Transcript & Mutation Effects

hg38 • Region Span ~22.9 kb

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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 SAGE1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 112

SAGE1-related disorderTotal: 15

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001381902.1. 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	8 clinvar		9
missense			95 clinvar	24 clinvar	5 clinvar	124
nonsense			3 clinvar			3
start loss						0
frameshift				1 clinvar		1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	101	33	5	139

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 11 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001381902.1	RefSeq	NP_001368831.1	19	MANE Select
ENST00000370709.4	Ensembl	ENSP00000359743.3	19	MANE Select
NM_018666.3	RefSeq	NP_061136.2	19	Standard
ENST00000324447.8	Ensembl	ENSP00000323191.3	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

snRNA 3'-end processing

Cellular Component

nucleus
nucleoplasm
integrator complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000535938
Coding exons: 19
Length: 23847
Individuals with no LoFs: 125643
Homozygous LoFs: 33
Heterozygous LoFs: 36
Defined: 125712
p: 0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.390	370	349	1.06	0.0000257	5977
Missense (PolyPhen)		102	112.5	0.90664		2188
Synonymous	-0.0990	127	126	1.01	0.0000100	1733
Loss of Function	0.227	27	28.3	0.954	0.00000222	480

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000076	0.000062	rare
Latino/Admixed American	0.00040	0.00032	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00023	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00020	0.00014	rare
South Asian	0.0020	0.0012	notable
Other	0.00048	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.947
RVIS EVS: 0.01
RVIS percentile EVS: 54.1

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0147

Gene Damage Prediction

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