SRA1

steroid receptor RNA activator 1

Basic information

Region (hg38): 5:140537340-140557677

Links

ENSG00000213523 ∙ NCBI:10011 ∙ OMIM:603819 ∙ HGNC:11281 ∙ Uniprot:Q9HD15 ∙ 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 SRA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRA1 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				5	5	10
missense			30	5	4	39
nonsense						0
start loss						0
frameshift			1		2	3
inframe indel					1	1
splice donor/acceptor (+/-2bp)						0
splice region				1	1	2
non coding			5	2	5	12
Total	0	0	36	12	17

Variants in SRA1

This is a list of pathogenic ClinVar variants found in the SRA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-140537517-C-G			Benign (Apr 05, 2018)
5-140537578-A-G		not specified	Uncertain significance (Sep 05, 2024)
5-140539380-C-T		not specified	Uncertain significance (Apr 07, 2023)
5-140542185-C-T		not specified	Uncertain significance (Jun 11, 2021)
5-140542191-T-G		not specified	Uncertain significance (Jul 16, 2024)
5-140542220-C-A		not specified	Uncertain significance (Oct 10, 2023)
5-140542220-C-G		not specified	Uncertain significance (Mar 16, 2022)
5-140542230-C-G		not specified	Uncertain significance (Oct 03, 2024)
5-140542238-A-G		not specified	Uncertain significance (Sep 20, 2023)
5-140542253-C-T		not specified	Uncertain significance (Aug 12, 2021)
5-140547801-A-C		not specified	Uncertain significance (Apr 13, 2022)
5-140548907-C-A		not specified	Uncertain significance (Feb 28, 2024)
5-140548919-C-G		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
5-140548926-C-T		not specified	Uncertain significance (Jan 04, 2024)
5-140548927-G-A		not specified	Uncertain significance (Aug 10, 2021)
5-140548927-G-T		not specified	Uncertain significance (Jul 05, 2024)
5-140548928-A-C		not specified	Uncertain significance (Jan 20, 2023)
5-140548997-C-T		not specified	Uncertain significance (Dec 05, 2022)
5-140548999-G-A		not specified	Uncertain significance (Jul 14, 2021)
5-140549026-T-C		not specified	Likely benign (Feb 13, 2023)
5-140549053-A-T		not specified	Uncertain significance (Sep 30, 2021)
5-140549057-G-A		not specified	Uncertain significance (Jun 06, 2023)
5-140549239-G-A		not specified	Uncertain significance (May 16, 2024)
5-140550722-G-A		SRA1-related disorder	Benign (Nov 27, 2023)
5-140550729-T-C		not specified	Uncertain significance (Jun 11, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRA1	protein_coding	protein_coding	ENST00000336283	5	20971

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000519	0.438	125721	0	27	125748	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.331	142	131	1.08	0.00000679	1472
Missense in Polyphen		59	51.524	1.1451		621
Synonymous	-0.208	52	50.1	1.04	0.00000245	479
Loss of Function	0.535	9	10.9	0.825	5.50e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000905	0.0000904
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000142	0.000141
Middle Eastern	0.000164	0.000163
South Asian	0.000163	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Functional RNA which acts as a transcriptional coactivator that selectively enhances steroid receptor-mediated transactivation ligand-independently through a mechanism involving the modulating N-terminal domain (AF-1) of steroid receptors. Also mediates transcriptional coactivation of steroid receptors ligand- dependently through the steroid-binding domain (AF-2). Enhances cellular proliferation and differentiation and promotes apoptosis in vivo. May play a role in tumorigenesis. {ECO:0000269|PubMed:10199399, ECO:0000269|PubMed:12943696, ECO:0000269|PubMed:14517287, ECO:0000269|PubMed:15147866, ECO:0000269|PubMed:15351741}.
• Pathway: mechanism of gene regulation by peroxisome proliferators via ppara;Validated nuclear estrogen receptor alpha network (Consensus)

Recessive Scores

• pRec: 0.0882

Intolerance Scores

• loftool: 0.966
• rvis_EVS: 0.6
• rvis_percentile_EVS: 82.66

Haploinsufficiency Scores

• pHI: 0.358
• hipred: Y
• hipred_score: 0.550
• ghis: 0.429

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 1.00

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	High	High	High
Primary Immunodeficiency	High	High	High
Cancer	High	High	High

Mouse Genome Informatics

• Gene name: Sra1
• Phenotype: nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); immune system phenotype; skeleton phenotype; renal/urinary system phenotype; liver/biliary system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan)

Zebrafish Information Network

• Gene name: sra1
• Affected structure: pericardium
• Phenotype tag: abnormal
• Phenotype quality: edematous

Gene ontology

• Biological process: regulation of transcription by RNA polymerase II;apoptotic process;cell population proliferation;cell differentiation;regulation of apoptotic process;negative regulation of myoblast differentiation;cellular response to estrogen stimulus;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;microtubule cytoskeleton;intercellular bridge;ribonucleoprotein complex
• Molecular function: steroid receptor RNA activator RNA binding;transcription coactivator activity;protein binding;nuclear receptor transcription coactivator activity