SNW1
SNW domain containing 1, the group of Spliceosomal B complex|Spliceosomal Bact complex|Spliceosomal P complex|NTC associated proteins|Spliceosomal C complex
Basic information
Region (hg38): 14:77717599-77761207
Previous symbols: [ "SKIIP" ]
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SNW1 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 | 16 | 16 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 16 | 0 | 0 |
Variants in SNW1
This is a list of pathogenic ClinVar variants found in the SNW1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 14-77718143-T-A | not specified | Uncertain significance (Sep 11, 2024) | ||
| 14-77718251-C-T | not specified | Uncertain significance (Oct 02, 2023) | ||
| 14-77718263-G-C | not specified | Uncertain significance (Mar 16, 2024) | ||
| 14-77718439-A-G | not specified | Uncertain significance (Nov 22, 2023) | ||
| 14-77718509-C-A | not specified | Uncertain significance (Jun 10, 2024) | ||
| 14-77720751-T-C | not specified | Uncertain significance (May 17, 2023) | ||
| 14-77720761-G-A | not specified | Uncertain significance (Dec 10, 2024) | ||
| 14-77720805-T-C | not specified | Uncertain significance (Apr 01, 2022) | ||
| 14-77723221-G-C | not specified | Uncertain significance (Jul 25, 2023) | ||
| 14-77723262-C-T | not specified | Uncertain significance (May 06, 2024) | ||
| 14-77731109-C-T | not specified | Uncertain significance (Jan 18, 2023) | ||
| 14-77732501-T-C | not specified | Uncertain significance (Feb 27, 2024) | ||
| 14-77732546-G-A | not specified | Uncertain significance (Apr 07, 2022) | ||
| 14-77736990-T-C | not specified | Uncertain significance (May 21, 2024) | ||
| 14-77737003-C-T | not specified | Uncertain significance (Aug 04, 2021) | ||
| 14-77737025-C-A | Uncertain significance (Nov 01, 2017) | |||
| 14-77738811-G-A | not specified | Uncertain significance (Nov 20, 2024) | ||
| 14-77738836-C-T | not specified | Uncertain significance (Jan 05, 2022) | ||
| 14-77751348-T-C | not specified | Uncertain significance (Oct 05, 2023) | ||
| 14-77751354-C-T | not specified | Uncertain significance (Dec 27, 2022) | ||
| 14-77751356-T-G | not specified | Uncertain significance (Dec 15, 2022) | ||
| 14-77751445-A-C | not specified | Uncertain significance (Jun 02, 2024) | ||
| 14-77751457-A-C | not specified | Uncertain significance (Feb 11, 2022) | ||
| 14-77754995-C-T | not specified | Uncertain significance (Jul 10, 2024) | ||
| 14-77755002-C-T | not specified | Uncertain significance (Aug 27, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SNW1 | protein_coding | protein_coding | ENST00000261531 | 14 | 43609 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000387 | 125741 | 0 | 7 | 125748 | 0.0000278 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.85 | 169 | 310 | 0.544 | 0.0000174 | 3525 |
| Missense in Polyphen | 20 | 73.983 | 0.27033 | 870 | ||
| Synonymous | 1.40 | 84 | 102 | 0.824 | 0.00000545 | 991 |
| Loss of Function | 5.08 | 3 | 35.8 | 0.0838 | 0.00000217 | 388 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.0000994 | 0.0000992 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.0000464 | 0.0000462 |
| European (Non-Finnish) | 0.0000354 | 0.0000352 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- 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}.;
- Pathway
- 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;RIG-I-like Receptor Signaling;Splicing factor NOVA regulated synaptic proteins;Notch Signaling Pathway;Notch;Disease;RUNX3 regulates NOTCH signaling;Signal Transduction;Gene expression (Transcription);Transcriptional regulation by RUNX3;Generic Transcription Pathway;RNA Polymerase II Transcription;Metabolism of RNA;Notch-HLH transcription pathway;NICD traffics to nucleus;mRNA Splicing - Major Pathway;SMAD2/SMAD3:SMAD4 heterotrimer regulates transcription;Pre-NOTCH Transcription and Translation;Pre-NOTCH Expression and Processing;Signaling by NOTCH1;NOTCH3 Intracellular Domain Regulates Transcription;Signaling by NOTCH3;Signaling by NOTCH;TGF_beta_Receptor;Transcriptional activity of SMAD2/SMAD3:SMAD4 heterotrimer;Constitutive Signaling by NOTCH1 PEST Domain Mutants;Signaling by NOTCH1 PEST Domain Mutants in Cancer;Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants;Signaling by NOTCH1 HD+PEST Domain Mutants in Cancer;Signaling by NOTCH1 in Cancer;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;Diseases of signal transduction;mRNA Splicing;NOTCH1 Intracellular Domain Regulates Transcription;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.156
Intolerance Scores
- loftool
- 0.180
- rvis_EVS
- -0.49
- rvis_percentile_EVS
- 22.09
Haploinsufficiency Scores
- pHI
- 0.875
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.687
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 1.00
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Snw1
- Phenotype
Zebrafish Information Network
- Gene name
- snw1
- Affected structure
- neural crest cell
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- 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;positive regulation of transcription of Notch receptor target;viral process;positive regulation of transforming growth factor beta receptor signaling pathway;intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator;positive regulation by host of viral transcription;positive regulation of Notch signaling pathway;negative regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II;positive regulation of mRNA splicing, via spliceosome;retinoic acid receptor signaling pathway;regulation of retinoic acid receptor signaling pathway;positive regulation of neurogenesis;positive regulation of histone H3-K4 methylation;regulation of vitamin D receptor signaling pathway;positive regulation of vitamin D receptor signaling pathway;cellular response to retinoic acid
- Cellular component
- nucleus;nucleoplasm;spliceosomal complex;cyclin/CDK positive transcription elongation factor complex;nuclear matrix;nuclear body;nuclear speck;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome
- Molecular function
- transcription coactivator activity;transcription corepressor activity;RNA binding;Notch binding;protein binding;enzyme binding;nuclear hormone receptor binding;vitamin D receptor binding;retinoic acid receptor binding;SMAD binding;androgen receptor binding