GeneBe

SNW1

protein-coding

SNW domain containing 1, the group of Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins|Spliceosomal C complex

Gene summary

This gene, a member of the SNW gene family, encodes a coactivator that enhances transcription from some Pol II promoters. This coactivator can bind to the ligand-binding domain of the vitamin D receptor and to retinoid receptors to enhance vitamin D-, retinoic acid-, estrogen-, and glucocorticoid-mediated gene expression. It can also function as a splicing factor by interacting with poly(A)-binding protein 2 to directly control the expression of muscle-specific genes at the transcriptional level. Finally, the protein may be involved in oncogenesis since it interacts with a region of SKI oncoproteins that is required for transforming activity. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]

Previous symbols:
  • SKIIP

MANE transcript

NM_012245.3

Inheritance

—

ClinVar variants

U:54

Top phenotype

SNW1-associated neurodevelopmental disorder

gnomAD constraint

pLI —, LoF o/e 0.08

Max pathogenic AF

—

Genomic locus

chr14:77,717,599-77,761,207

External References & Databases

Ensembl (ENSG00000100603)NCBI Gene (22938)OMIM (603055)HGNC:16696GenCCUniProt (Q13573)AlphaFoldClinVar (SNW1)gnomADPubMedJAXSFARI

Transcript & Mutation Effects

hg38 • Region Span ~43.6 kb
Loading mutation effect viewer...

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 SNW1 variants in ClinVar

3 Conditions Cataloged
not specifiedTotal: 39
not providedTotal: 6
SNW1-associated neurodevelopmental disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_012245.3. 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.

EffectPLPVUSLBBSum
synonymous
2
clinvar
 2
missense
44
clinvar
 44
nonsense
1
clinvar
 1
start loss
0
frameshift
1
clinvar
 1
splice donor/acceptor (+/-2bp)
6
clinvar
 6
Total00540054
Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_012245.3RefSeqNP_036377.114MANE Select
ENST00000261531.12EnsemblENSP00000261531.814MANE Select
NM_001318844.2RefSeqNP_001305773.113Standard
ENST00000554324.1EnsemblENSP00000452473.16Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
snw1Danio rerio

Structure: neural crest cell

Quality: decreased amount

abnormal

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

  • Viral carcinogenesis - Homo sapiens (human)
  • Spliceosome - Homo sapiens (human)
  • Notch signaling pathway - Homo sapiens (human)
  • Epstein-Barr virus infection - Homo sapiens (human)
  • TGF-beta Signaling Pathway

Biological Process

  • negative regulation of transcription by RNA polymerase II
  • mRNA splicing, via spliceosome
  • regulation of transcription by RNA polymerase II
  • transcription initiation from RNA polymerase II promoter
  • Notch signaling pathway

Molecular Function

  • transcription coactivator activity
  • transcription corepressor activity
  • RNA binding
  • Notch binding
  • protein binding

Cellular Component

  • nucleus
  • nucleoplasm
  • spliceosomal complex
  • cyclin/CDK positive transcription elongation factor complex
  • nuclear matrix

gnomAD Constraint

Source: gnomAD

Gene type
protein_coding
Transcript type
protein_coding
Transcript
ENST00000261531
Coding exons
14
Length
43609
Individuals with no LoFs
125741
Homozygous LoFs
0
Heterozygous LoFs
7
Defined
125748
p
0.0000278
Z-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense2.851693100.5440.00001743525
Missense (PolyPhen)2073.9830.27033870
Synonymous1.40841020.8240.00000545991
Loss of Function5.08335.80.08380.00000217388

Population LoF Frequency

PopulationCAFp-valueStatus
African00.0absent
Latino/Admixed American00.0absent
Ashkenazi Jewish0.0000990.000099rare
East Asian0.0000540.000054rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.0000350.000035rare
South Asian00.0absent
Other00.0absent

dbNSFP Gene Annotations

Source: dbNSFP

Function
FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346). Is required in the specific splicing of CDKN1A pre-mRNA; the function probably involves the recruitment of U2AF2 to the mRNA. Is proposed to recruit PPIL1 to the spliceosome. May be involved in cyclin-D1/CCND1 mRNA stability through the SNARP complex which associates with both the 3'end of the CCND1 gene and its mRNA. Involved in transcriptional regulation. Modulates TGF-beta- mediated transcription via association with SMAD proteins, MYOD1- mediated transcription via association with PABPN1, RB1-mediated transcriptional repression, and retinoid-X receptor (RXR)- and vitamin D receptor (VDR)-dependent gene transcription in a cell line-specific manner probably involving coactivators NCOA1 and GRIP1. Is involved in NOTCH1-mediated transcriptional activation. Binds to multimerized forms of Notch intracellular domain (NICD) and is proposed to recruit transcriptional coactivators such as MAML1 to form an intermediate preactivation complex which associates with DNA-bound CBF-1/RBPJ to form a transcriptional activation complex by releasing SNW1 and redundant NOTCH1 NICD. {ECO:0000269|PubMed:10644367, ECO:0000269|PubMed:11278756, ECO:0000269|PubMed:11371506, ECO:0000269|PubMed:11514567, ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:12840015, ECO:0000269|PubMed:14985122, ECO:0000269|PubMed:15194481, ECO:0000269|PubMed:15905409, ECO:0000269|PubMed:18794151, ECO:0000269|PubMed:19818711, ECO:0000269|PubMed:21245387, ECO:0000269|PubMed:21460037, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770, ECO:0000269|PubMed:9632709}.; FUNCTION: (Microbial infection) Proposed to be involved in transcriptional activation by EBV EBNA2 of CBF-1/RBPJ-repressed promoters. {ECO:0000269|PubMed:10644367}.;

Recessive Scores

pRec
0.156

Intolerance Scores

LoFtool
0.180
RVIS EVS
-0.49
RVIS percentile EVS
22.09

Essentials

Essential (CRISPR)
N
Essential (CRISPR2)
E
Essential (gene trap)
E
Indispensability pred.
E
Indispensability score
1.00

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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