SAGE1

sarcoma antigen 1, the group of SAGE family

Basic information

Region (hg38): X:135890182-135913062

Links

ENSG00000181433 ∙ NCBI:55511 ∙ OMIM:300359 ∙ HGNC:30369 ∙ Uniprot:Q9NXZ1 ∙ 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 SAGE1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAGE1 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				2		2
missense			49	9		58
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	49	11	0

Variants in SAGE1

This is a list of pathogenic ClinVar variants found in the SAGE1 region.

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

Position	Type	Phenotype	Significance	ClinVar
X-135896258-C-G		not specified	Uncertain significance (Jan 05, 2022)
X-135896266-G-A		SAGE1-related disorder	Benign (Oct 23, 2019)
X-135896274-C-T		SAGE1-related disorder	Benign (Apr 16, 2019)
X-135901610-A-C		not specified	Uncertain significance (May 01, 2022)
X-135901669-C-T			Likely benign (Jun 01, 2022)
X-135904497-A-G		not specified	Likely benign (Dec 13, 2021)
X-135904514-A-G		not specified	Likely benign (Feb 28, 2024)
X-135904533-G-A		not specified	Uncertain significance (Mar 15, 2024)
X-135904537-A-G		not specified	Uncertain significance (Dec 06, 2021)
X-135904541-T-C		SAGE1-related disorder	Benign (Oct 23, 2019)
X-135904545-T-C		SAGE1-related disorder	Likely benign (May 10, 2019)
X-135905287-A-T		not specified	Uncertain significance (Dec 21, 2022)
X-135905332-C-T		not specified	Likely benign (May 21, 2024)
X-135905333-C-T		not specified	Uncertain significance (Feb 01, 2025)
X-135905354-C-T		not specified	Uncertain significance (Jan 23, 2023)
X-135905375-T-C		not specified	Uncertain significance (Jan 08, 2025)
X-135906038-C-CA		SAGE1-related disorder	Likely benign (Jun 06, 2021)
X-135906419-G-A		not specified	Uncertain significance (Feb 26, 2025)
X-135906422-A-G		not specified	Uncertain significance (Jul 08, 2022)
X-135906447-T-C		not specified	Uncertain significance (Feb 28, 2024)
X-135906476-G-A		not specified	Uncertain significance (May 02, 2023)
X-135906491-C-T			not provided (-)
X-135906498-G-A		not specified	Likely benign (Sep 03, 2024)
X-135906500-C-T		not specified	Uncertain significance (Jul 11, 2023)
X-135906501-G-T		not specified	Likely benign (Jan 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAGE1	protein_coding	protein_coding	ENST00000535938	19	23847

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
8.57e-18	0.00842	125643	33	36	125712	0.000274

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.390	370	349	1.06	0.0000257	5977
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000481	0.000466
Ashkenazi Jewish	0.00	0.00
East Asian	0.000226	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000201	0.000141
Middle Eastern	0.000226	0.000163
South Asian	0.00199	0.00118
Other	0.000475	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.947
• rvis_EVS: 0.01
• rvis_percentile_EVS: 54.1

Haploinsufficiency Scores

• pHI: 0.434
• hipred: N
• hipred_score: 0.112
• ghis: 0.384

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0147

Gene Damage Prediction

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

Gene ontology

• Biological process: snRNA 3'-end processing
• Cellular component: nucleus;nucleoplasm;integrator complex