SRRT

serrate, RNA effector molecule

Basic information

Region (hg38): 7:100875103-100888664

Links

ENSG00000087087 ∙ NCBI:51593 ∙ OMIM:614469 ∙ HGNC:24101 ∙ Uniprot:Q9BXP5 ∙ 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 SRRT gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRRT 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	5	7
missense			56	1		57
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding					2	2
Total	0	0	56	3	7

Variants in SRRT

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

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

Position	Type	Phenotype	Significance	ClinVar
7-100881319-G-A		not specified	Uncertain significance (Dec 09, 2024)
7-100881346-C-T		not specified	Uncertain significance (May 07, 2024)
7-100881355-C-T		not specified	Uncertain significance (Nov 25, 2024)
7-100881371-G-A		not specified	Uncertain significance (Nov 01, 2022)
7-100881398-G-C		not specified	Uncertain significance (Dec 17, 2021)
7-100881712-G-C		not specified	Uncertain significance (Jan 23, 2024)
7-100881764-C-T			Likely benign (Mar 01, 2023)
7-100882125-C-T			Benign (Dec 11, 2018)
7-100884097-G-A			Benign (Dec 31, 2019)
7-100884114-A-G		not specified	Uncertain significance (Sep 02, 2024)
7-100884122-C-T		not specified	Uncertain significance (Jan 22, 2024)
7-100884123-G-A		not specified	Uncertain significance (Jul 14, 2021)
7-100884146-A-T		not specified	Uncertain significance (Aug 02, 2023)
7-100884176-T-C		not specified	Uncertain significance (Oct 12, 2024)
7-100884218-A-G		not specified	Uncertain significance (May 13, 2024)
7-100884392-C-T		not specified	Uncertain significance (Aug 05, 2024)
7-100884405-T-C			Benign (Apr 03, 2020)
7-100884407-G-A		not specified	Uncertain significance (Sep 20, 2023)
7-100884457-C-T		not specified	Uncertain significance (Nov 10, 2024)
7-100884461-G-A		not specified	Uncertain significance (Dec 17, 2024)
7-100884473-A-G		not specified	Uncertain significance (Jun 16, 2024)
7-100884502-G-A		not specified	Uncertain significance (Feb 22, 2025)
7-100884508-C-T		not specified	Uncertain significance (May 17, 2024)
7-100884509-G-A		not specified	Uncertain significance (Dec 17, 2024)
7-100884527-A-C		not specified	Uncertain significance (Jul 29, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRRT	protein_coding	protein_coding	ENST00000347433	19	13553

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.594	0.406	125714	0	34	125748	0.000135

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.97	383	585	0.655	0.0000392	5771
Missense in Polyphen		101	183.18	0.55137		1828
Synonymous	-2.09	266	226	1.18	0.0000152	1649
Loss of Function	4.97	10	46.7	0.214	0.00000242	529

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000575	0.000572
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.000109	0.000109
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.000109	0.000109
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Acts as a mediator between the cap-binding complex (CBC) and the primary microRNAs (miRNAs) processing machinery during cell proliferation. Contributes to the stability and delivery of capped primary miRNA transcripts to the primary miRNA processing complex containing DGCR8 and DROSHA, thereby playing a role in RNA-mediated gene silencing (RNAi) by miRNAs. Binds capped RNAs (m7GpppG-capped RNA); however interaction is probably mediated via its interaction with NCBP1/CBP80 component of the CBC complex. Involved in cell cycle progression at S phase. Does not directly confer arsenite resistance but rather modulates arsenic sensitivity. Independently of its activity on miRNAs, necessary and sufficient to promote neural stem cell self-renewal. Does so by directly binding SOX2 promoter and positively regulating its transcription (By similarity). {ECO:0000250, ECO:0000269|PubMed:19632182}.
• Pathway: Gene expression (Transcription);RNA polymerase II transcribes snRNA genes;RNA Polymerase II Transcription;Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Intolerance Scores

• loftool: 0.0688
• rvis_EVS: -1.59
• rvis_percentile_EVS: 3.05

Haploinsufficiency Scores

• hipred: Y
• hipred_score: 0.563
• ghis: 0.681

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.847

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srrt
• Phenotype: endocrine/exocrine gland phenotype; cellular phenotype; hematopoietic system 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); embryo phenotype; immune system phenotype

Zebrafish Information Network

• Gene name: srrt
• Affected structure: mandibular arch skeleton
• Phenotype tag: abnormal
• Phenotype quality: increased thickness

Gene ontology

• Biological process: mRNA splicing, via spliceosome;regulation of transcription, DNA-templated;cell population proliferation;primary miRNA processing;snRNA transcription by RNA polymerase II;response to arsenic-containing substance;positive regulation of neurogenesis;neuronal stem cell population maintenance
• Cellular component: nucleoplasm;cytoplasm;protein-containing complex
• Molecular function: DNA binding;RNA binding;protein binding