SAP30
Basic information
Region (hg38): 4:173369969-173377532
Links
Phenotypes
GenCC
Source:
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 SAP30 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 | 15 | 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 | 15 | 0 | 0 |
Variants in SAP30
This is a list of pathogenic ClinVar variants found in the SAP30 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 4-173371198-C-T | not specified | Uncertain significance (May 01, 2022) | ||
| 4-173371244-C-T | not specified | Uncertain significance (Feb 28, 2023) | ||
| 4-173371292-G-A | not specified | Uncertain significance (Oct 11, 2024) | ||
| 4-173371321-G-A | not specified | Uncertain significance (Dec 02, 2024) | ||
| 4-173371346-C-T | not specified | Uncertain significance (Jan 08, 2024) | ||
| 4-173371354-G-A | not specified | Uncertain significance (Feb 27, 2024) | ||
| 4-173371357-G-A | not specified | Uncertain significance (Nov 25, 2024) | ||
| 4-173371378-C-G | not specified | Uncertain significance (Sep 17, 2021) | ||
| 4-173373504-G-C | not specified | Uncertain significance (Dec 16, 2023) | ||
| 4-173373992-C-A | not specified | Uncertain significance (Sep 03, 2024) | ||
| 4-173373997-T-C | not specified | Uncertain significance (Jul 19, 2023) | ||
| 4-173374006-G-A | not specified | Uncertain significance (Jun 16, 2023) | ||
| 4-173377251-C-T | not specified | Uncertain significance (Jan 31, 2024) | ||
| 4-173377260-A-G | not specified | Uncertain significance (Sep 14, 2022) | ||
| 4-173377313-A-G | not specified | Uncertain significance (Aug 01, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SAP30 | protein_coding | protein_coding | ENST00000296504 | 4 | 7564 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.310 | 0.674 | 125662 | 0 | 7 | 125669 | 0.0000279 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.885 | 77 | 102 | 0.754 | 0.00000449 | 1401 |
| Missense in Polyphen | 25 | 49.132 | 0.50883 | 653 | ||
| Synonymous | -0.0455 | 41 | 40.6 | 1.01 | 0.00000184 | 441 |
| Loss of Function | 2.02 | 2 | 8.29 | 0.241 | 4.23e-7 | 106 |
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) | 0.0000570 | 0.0000528 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000329 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the functional recruitment of the Sin3- histone deacetylase complex (HDAC) to a specific subset of N-CoR corepressor complexes. Capable of transcription repression by N- CoR. Active in deacetylating core histone octamers (when in a complex) but inactive in deacetylating nucleosomal histones. {ECO:0000250|UniProtKB:O88574, ECO:0000269|PubMed:9651585}.;
- Pathway
- Retinoblastoma (RB) in Cancer;Notch Signaling Pathway;Notch;NoRC negatively regulates rRNA expression;Negative epigenetic regulation of rRNA expression;Epigenetic regulation of gene expression;Gene expression (Transcription);HDACs deacetylate histones;Chromatin modifying enzymes;Chromatin organization;Regulation of Telomerase;Signaling events mediated by HDAC Class I;Hedgehog signaling events mediated by Gli proteins;Regulation of nuclear SMAD2/3 signaling
(Consensus)
Recessive Scores
- pRec
- 0.112
Intolerance Scores
- loftool
- 0.510
- rvis_EVS
- 0.06
- rvis_percentile_EVS
- 58
Haploinsufficiency Scores
- pHI
- 0.229
- hipred
- Y
- hipred_score
- 0.640
- ghis
- 0.579
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.914
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Sap30
- Phenotype
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;regulation of transcription, DNA-templated;histone deacetylation;skeletal muscle cell differentiation
- Cellular component
- histone deacetylase complex;nucleoplasm
- Molecular function
- DNA binding;transcription corepressor activity;histone deacetylase activity;protein binding;metal ion binding