SRRM1

protein-coding

serine and arginine repetitive matrix 1

Gene summary

Enables RNA binding activity. Predicted to be involved in regulation of mRNA splicing, via spliceosome. Located in nuclear speck. Part of catalytic step 2 spliceosome. Biomarker of gestational diabetes. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_005839.4

Inheritance

—

ClinVar variants

U:119B:4

Top phenotype

Neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr1:24,631,716-24,673,281

External References & Databases

Ensembl (ENSG00000133226)

Transcript & Mutation Effects

hg38 • Region Span ~41.6 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 SRRM1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 111

Neurodevelopmental disorderTotal: 3

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_005839.4. 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			3 clinvar	2 clinvar		5
missense			109 clinvar	2 clinvar		111
nonsense			4 clinvar			4
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	119	4	0	123

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 168 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_005839.4	RefSeq	NP_005830.2	17	MANE Select
ENST00000323848.14	Ensembl	ENSP00000326261.8	17	MANE Select
NM_001303448.2	RefSeq	NP_001290377.1	18	Standard
NM_001303449.1	RefSeq	NP_001290378.1	16	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

mRNA surveillance pathway - Homo sapiens (human)
RNA transport - Homo sapiens (human)
mRNA Processing
Gene expression (Transcription)
RNA Polymerase II Transcription

Biological Process

RNA splicing, via transesterification reactions
mRNA splicing, via spliceosome
RNA export from nucleus
mRNA export from nucleus
RNA splicing

Molecular Function

DNA binding
RNA binding
protein binding

Cellular Component

nucleus
nucleoplasm
cytosol
nuclear matrix
nuclear speck

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000323848
Coding exons: 17
Length: 41552
Individuals with no LoFs: 125718
Homozygous LoFs: 0
Heterozygous LoFs: 29
Defined: 125747
p: 0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.46	426	519	0.820	0.0000339	5658
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00051	0.00049	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.000045	0.000044	rare
South Asian	0.000043	0.000033	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.113

Intolerance Scores

LoFtool: 0.413
RVIS EVS: -0.93
RVIS percentile EVS: 9.68

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): E
Indispensability pred.: E
Indispensability score: 0.925

Gene Damage Prediction

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