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.

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.

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						0
missense			35	4		39
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region						0
non coding						0
Total	0	0	36	4	0

Variants in SRRM4

This is a list of pathogenic ClinVar variants found in the SRRM4 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-118981899-A-G		not specified	Uncertain significance (Jan 05, 2022)
12-119102244-C-T			Likely benign (Apr 01, 2024)
12-119102271-A-G		not specified	Likely benign (Jan 30, 2024)
12-119102304-T-G		not specified	Uncertain significance (Sep 01, 2021)
12-119102354-C-T		not specified	Uncertain significance (Aug 23, 2021)
12-119102372-A-G		not specified	Uncertain significance (Jul 14, 2022)
12-119114278-T-G		not specified	Uncertain significance (Jul 06, 2022)
12-119114321-G-C		not specified	Uncertain significance (Oct 04, 2022)
12-119114330-A-G		not specified	Uncertain significance (Jun 07, 2023)
12-119114348-C-T		not specified	Uncertain significance (Apr 23, 2024)
12-119114349-G-A		not specified	Uncertain significance (Sep 26, 2023)
12-119117000-G-T		not specified	Uncertain significance (Dec 01, 2022)
12-119120278-T-C			Uncertain significance (Jul 01, 2017)
12-119125398-G-A		not specified	Uncertain significance (Feb 15, 2023)
12-119125427-T-C		not specified	Uncertain significance (Mar 27, 2023)
12-119125437-G-A		not specified	Uncertain significance (Nov 05, 2021)
12-119130682-C-T		not specified	Uncertain significance (Jan 09, 2024)
12-119130685-G-A		not specified	Uncertain significance (Aug 08, 2022)
12-119130715-C-T		not specified	Uncertain significance (Feb 01, 2023)
12-119130730-C-T		not specified	Uncertain significance (Oct 06, 2021)
12-119130733-C-T		not specified	Uncertain significance (Dec 13, 2023)
12-119130734-G-A		not specified	Uncertain significance (Mar 28, 2023)
12-119130785-C-T		not specified	Uncertain significance (Mar 26, 2024)
12-119145385-C-T		not specified	Uncertain significance (Oct 12, 2022)
12-119145432-C-A		not specified	Uncertain significance (Oct 26, 2022)

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
0.465	0.535	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

Haploinsufficiency Scores

• pHI: 0.354
• hipred: Y
• hipred_score: 0.663
• ghis: 0.526

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

Mouse Genome Informatics

• Gene name: Srrm4
• Phenotype: homeostasis/metabolism phenotype; cellular 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system 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); hearing/vestibular/ear phenotype

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