SRRM4

serine/arginine repetitive matrix 4

Basic information

Region (hg38): 12:118981541-119163051

Previous symbols: [ "KIAA1853" ]

Links

ENSG00000139767 ∙ NCBI:84530 ∙ OMIM:613103 ∙ HGNC:29389 ∙ Uniprot:A7MD48 ∙ 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 SRRM4 gene.

• not_specified (94 variants)
• not_provided (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SRRM4 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000194286.4. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1			1
missense			92	4		96
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1			1
Total	0	0	94	4	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SRRM4	protein_coding	protein_coding	ENST00000267260	13	181557

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
		124630	0	11	124641	0.0000441

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	311	388	0.801	0.0000262	3885
Missense in Polyphen		71	99.047	0.71683		951
Synonymous	0.209	141	144	0.978	0.00000794	1252
Loss of Function	4.10	7	32.0	0.218	0.00000203	350

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000951	0.0000949
Ashkenazi Jewish	0.00	0.00
East Asian	0.000112	0.000111
Finnish	0.00	0.00
European (Non-Finnish)	0.0000545	0.0000531
Middle Eastern	0.000112	0.000111
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Splicing factor specifically required for neural cell differentiation. Acts in conjunction with nPTB/PTBP2 by binding directly to its regulated target transcripts and promotes neural- specific exon inclusion in many genes that function in neural cell differentiation. Required to promote the inclusion of neural- specific exon 10 in nPTB/PTBP2, leading to increased expression of neural-specific nPTB/PTBP2. Also promotes the inclusion of exon 16 in DAAM1 in neuron extracts. Promotes alternative splicing of REST transcripts to produce a REST isoform (REST4) with greatly reduced repressive activity, thereby activating expression of REST targets in neural cells. Plays an important role during embryonic development as well as in the proper functioning of the adult nervous system. Regulates alternative splicing events in genes with important neuronal functions (By similarity). {ECO:0000250|UniProtKB:Q8BKA3}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.534
• rvis_EVS: 0.11
• rvis_percentile_EVS: 62.1

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.731

Gene Damage Prediction

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

Zebrafish Information Network

• Gene name: srrm4
• Affected structure: ventricular system
• Phenotype tag: abnormal
• Phenotype quality: increased volume

Gene ontology

• Biological process: regulation of alternative mRNA splicing, via spliceosome;mRNA processing;nervous system development;sensory perception of sound;RNA splicing;cell differentiation;neuron maturation;regulation of RNA splicing
• Cellular component: nucleus
• Molecular function: mRNA binding