SARNP
SAP domain containing ribonucleoprotein, the group of Transcription and export complex 1 subunits
Basic information
Region (hg38): 12:55752463-55817724
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 SARNP 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 | 14 | 15 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 1 | 0 |
Variants in SARNP
This is a list of pathogenic ClinVar variants found in the SARNP region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 12-55757552-G-C | not specified | Uncertain significance (Oct 29, 2024) | ||
| 12-55757553-C-G | not specified | Uncertain significance (Aug 27, 2024) | ||
| 12-55760570-C-G | not specified | Uncertain significance (May 24, 2023) | ||
| 12-55789084-G-C | not specified | Uncertain significance (Dec 11, 2023) | ||
| 12-55789091-G-A | not specified | Uncertain significance (Aug 02, 2021) | ||
| 12-55790568-A-G | not specified | Uncertain significance (Jun 04, 2024) | ||
| 12-55794365-T-C | not specified | Uncertain significance (Oct 10, 2023) | ||
| 12-55794816-C-T | not specified | Uncertain significance (Dec 01, 2022) | ||
| 12-55794832-T-C | not specified | Uncertain significance (Apr 25, 2022) | ||
| 12-55800583-G-T | not specified | Uncertain significance (Dec 14, 2023) | ||
| 12-55800629-C-T | not specified | Uncertain significance (Sep 22, 2023) | ||
| 12-55803635-C-T | not specified | Uncertain significance (Feb 26, 2024) | ||
| 12-55803659-G-C | not specified | Uncertain significance (Oct 29, 2024) | ||
| 12-55817688-G-A | not specified | Uncertain significance (Jul 26, 2024) | ||
| 12-55817695-T-C | not specified | Likely benign (Apr 22, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SARNP | protein_coding | protein_coding | ENST00000336133 | 11 | 65294 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.996 | 0.00426 | 125607 | 0 | 1 | 125608 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.18 | 72 | 106 | 0.678 | 0.00000518 | 1358 |
| Missense in Polyphen | 10 | 22.319 | 0.44805 | 299 | ||
| Synonymous | -0.957 | 43 | 35.7 | 1.20 | 0.00000163 | 382 |
| Loss of Function | 3.72 | 0 | 16.1 | 0.00 | 7.73e-7 | 207 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds both single-stranded and double-stranded DNA with higher affinity for the single-stranded form. Specifically binds to scaffold/matrix attachment region DNA. Also binds single- stranded RNA. Enhances RNA unwinding activity of DDX39A. May participate in important transcriptional or translational control of cell growth, metabolism and carcinogenesis. Component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA. TREX is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NFX1 pathway. The TREX complex is essential for the export of Kaposi's sarcoma-associated herpesvirus (KSHV) intronless mRNAs and infectious virus production. {ECO:0000269|PubMed:15338056, ECO:0000269|PubMed:17196963, ECO:0000269|PubMed:20844015}.;
- Pathway
- Gene expression (Transcription);RNA Polymerase II Transcription;Metabolism of RNA;Cleavage of Growing Transcript in the Termination Region ;RNA Polymerase II Transcription Termination;Transport of Mature mRNA derived from an Intron-Containing Transcript;mRNA 3,-end processing;Transport of Mature Transcript to Cytoplasm;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Intolerance Scores
- loftool
- rvis_EVS
- -0.12
- rvis_percentile_EVS
- 44.54
Haploinsufficiency Scores
- pHI
- hipred
- Y
- hipred_score
- 0.735
- ghis
- 0.636
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.965
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sarnp
- Phenotype
- hearing/vestibular/ear phenotype; immune system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype;
Gene ontology
- Biological process
- RNA export from nucleus;mRNA export from nucleus;regulation of translation;mRNA 3'-end processing
- Cellular component
- transcription export complex;nucleus;nucleoplasm;nuclear speck;cytoplasmic ribonucleoprotein granule
- Molecular function
- DNA binding;RNA binding;protein binding