SAFB
scaffold attachment factor B, the group of RNA binding motif containing
Basic information
Region (hg38): 19:5623034-5668478
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (5 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAFB gene is commonly pathogenic or not.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 6 | 6 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice variant | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 0 | 1 |
Variants in SAFB
This is a list of pathogenic ClinVar variants found in the SAFB region.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-5623288-C-G | Inborn genetic diseases | Uncertain significance (Aug 17, 2022) | ||
| 19-5641819-A-G | Inborn genetic diseases | Uncertain significance (May 05, 2023) | ||
| 19-5641923-C-G | Inborn genetic diseases | Uncertain significance (Dec 15, 2022) | ||
| 19-5645366-A-T | Inborn genetic diseases | Uncertain significance (Aug 12, 2021) | ||
| 19-5649932-C-T | Benign (Jul 17, 2018) | |||
| 19-5651007-G-A | Inborn genetic diseases | Uncertain significance (Mar 20, 2023) | ||
| 19-5654153-A-G | Inborn genetic diseases | Uncertain significance (May 15, 2023) | ||
| 19-5654435-A-C | Inborn genetic diseases | Uncertain significance (Nov 12, 2021) | ||
| 19-5657292-G-A | Inborn genetic diseases | Uncertain significance (May 26, 2023) | ||
| 19-5664027-A-T | Inborn genetic diseases | Uncertain significance (Dec 03, 2021) | ||
| 19-5664110-G-A | Inborn genetic diseases | Uncertain significance (Feb 16, 2023) | ||
| 19-5667105-G-C | Uncertain significance (Sep 11, 2017) | |||
| 19-5667107-G-A | Inborn genetic diseases | Uncertain significance (Apr 18, 2023) | ||
| 19-5667160-C-T | Inborn genetic diseases | Uncertain significance (May 23, 2023) | ||
| 19-5667871-G-A | Inborn genetic diseases | Uncertain significance (Jun 05, 2023) | ||
| 19-5668176-C-T | Inborn genetic diseases | Uncertain significance (May 31, 2023) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SAFB | protein_coding | protein_coding | ENST00000588852 | 21 | 45444 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000193 | 125715 | 0 | 1 | 125716 | 0.00000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.14 | 383 | 521 | 0.736 | 0.0000359 | 6002 |
| Missense in Polyphen | 78 | 137.23 | 0.5684 | 1753 | ||
| Synonymous | -2.11 | 234 | 196 | 1.19 | 0.0000134 | 1717 |
| Loss of Function | 5.98 | 2 | 45.6 | 0.0439 | 0.00000254 | 578 |
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) | 0.00000879 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Binds to scaffold/matrix attachment region (S/MAR) DNA and forms a molecular assembly point to allow the formation of a 'transcriptosomal' complex (consisting of SR proteins and RNA polymerase II) coupling transcription and RNA processing (By similarity). Can function as an estrogen receptor corepressor and can also bind to the HSP27 promoter and decrease its transcription. When associated with RBMX, binds to and stimulates transcription from the SREBF1 promoter (By similarity). Can inhibit cell proliferation. {ECO:0000250}.;
- Pathway
- Structural Pathway of Interleukin 1 (IL-1);Validated nuclear estrogen receptor alpha network
(Consensus)
Recessive Scores
- pRec
- 0.157
Intolerance Scores
- loftool
- 0.0204
- rvis_EVS
- -1.62
- rvis_percentile_EVS
- 2.93
Haploinsufficiency Scores
- pHI
- 0.207
- hipred
- Y
- hipred_score
- 0.743
- ghis
- 0.665
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- H
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.920
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Safb
- 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); reproductive system phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); liver/biliary system phenotype; respiratory system phenotype; skeleton phenotype; growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- chromatin organization;regulation of transcription by RNA polymerase II;intracellular estrogen receptor signaling pathway;regulation of growth;hormone metabolic process;positive regulation of transcription by RNA polymerase II;regulation of mRNA processing
- Cellular component
- nucleus;nucleoplasm
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;chromatin binding;double-stranded DNA binding;RNA binding;protein binding;sequence-specific DNA binding