SRRM1

serine and arginine repetitive matrix 1

Basic information

Region (hg38): 1:24631716-24673281

Links

ENSG00000133226 ∙ NCBI:10250 ∙ OMIM:605975 ∙ HGNC:16638 ∙ Uniprot:Q8IYB3 ∙ 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 SRRM1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRRM1 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				1		1
missense			60	1		61
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	61	2	0

Variants in SRRM1

This is a list of pathogenic ClinVar variants found in the SRRM1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-24646008-C-T		not specified	Uncertain significance (Sep 01, 2024)
1-24646676-A-T		not specified	Uncertain significance (Jan 23, 2025)
1-24649995-A-G		not specified	Uncertain significance (May 26, 2024)
1-24650005-A-C		not specified	Uncertain significance (Mar 06, 2025)
1-24650061-A-G		not specified	Uncertain significance (Mar 18, 2024)
1-24650082-A-G		not specified	Uncertain significance (Dec 15, 2022)
1-24651410-C-T		not specified	Uncertain significance (Mar 02, 2023)
1-24651510-G-A		not specified	Uncertain significance (Feb 19, 2025)
1-24651515-C-T		not specified	Uncertain significance (Jul 09, 2024)
1-24651560-G-C		not specified	Uncertain significance (Sep 09, 2024)
1-24651591-T-G		not specified	Uncertain significance (Dec 07, 2024)
1-24651602-A-G		not specified	Uncertain significance (Mar 07, 2024)
1-24652438-A-T		not specified	Uncertain significance (Jan 16, 2024)
1-24652483-C-A		not specified	Uncertain significance (Aug 08, 2022)
1-24652550-G-A		not specified	Uncertain significance (Jan 31, 2024)
1-24652574-G-A		not specified	Uncertain significance (Dec 26, 2023)
1-24652579-C-G		not specified	Uncertain significance (Sep 14, 2023)
1-24652580-G-A		not specified	Uncertain significance (Jan 29, 2024)
1-24652580-G-C		not specified	Uncertain significance (Jun 02, 2024)
1-24652585-C-T		not specified	Uncertain significance (Feb 22, 2023)
1-24652591-C-T		not specified	Uncertain significance (Jan 19, 2025)
1-24654884-G-C		not specified	Uncertain significance (Jun 17, 2024)
1-24654910-C-T		not specified	Uncertain significance (Sep 27, 2021)
1-24654959-C-T		not specified	Uncertain significance (Feb 16, 2023)
1-24655055-C-T		not specified	Uncertain significance (Aug 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRRM1	protein_coding	protein_coding	ENST00000323848	17	41552

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	5.83e-7	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.46	426	519	0.820	0.0000339	5658
Missense in Polyphen		4	43.363	0.092245		557
Synonymous	-1.76	214	184	1.17	0.00000995	1965
Loss of Function	6.38	3	53.2	0.0564	0.00000411	560

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000508	0.000508
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000231	0.000231
European (Non-Finnish)	0.0000445	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.0000430	0.0000327
Other	0.000165	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Part of pre- and post-splicing multiprotein mRNP complexes. Involved in numerous pre-mRNA processing events. Promotes constitutive and exonic splicing enhancer (ESE)-dependent splicing activation by bridging together sequence-specific (SR family proteins, SFRS4, SFRS5 and TRA2B/SFRS10) and basal snRNP (SNRP70 and SNRPA1) factors of the spliceosome. Stimulates mRNA 3'-end cleavage independently of the formation of an exon junction complex. Binds both pre-mRNA and spliced mRNA 20-25 nt upstream of exon-exon junctions. Binds RNA and DNA with low sequence specificity and has similar preference for either double- or single-stranded nucleic acid substrates. {ECO:0000269|PubMed:10339552, ECO:0000269|PubMed:10668804, ECO:0000269|PubMed:11739730, ECO:0000269|PubMed:12600940, ECO:0000269|PubMed:12944400, ECO:0000269|PubMed:9531537}.
• Pathway: mRNA surveillance pathway - Homo sapiens (human);RNA transport - Homo sapiens (human);mRNA Processing;Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;mRNA Splicing - Major Pathway;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA Splicing;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.413
• rvis_EVS: -0.93
• rvis_percentile_EVS: 9.68

Haploinsufficiency Scores

• pHI: 0.531
• hipred: Y
• hipred_score: 0.831
• ghis: 0.611

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.925

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Srrm1

Gene ontology

• Biological process: RNA splicing, via transesterification reactions;mRNA splicing, via spliceosome;RNA export from nucleus;mRNA export from nucleus;RNA splicing;mRNA 3'-end processing
• Cellular component: nucleus;nucleoplasm;cytosol;nuclear matrix;nuclear speck;catalytic step 2 spliceosome
• Molecular function: DNA binding;RNA binding;protein binding