SSBP2
Basic information
Region (hg38): 5:81412804-81751797
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 SSBP2 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 | 13 | 13 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 14 | 0 | 0 |
Variants in SSBP2
This is a list of pathogenic ClinVar variants found in the SSBP2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 5-81428674-T-C | not specified | Uncertain significance (May 05, 2023) | ||
| 5-81437440-C-G | Uncertain significance (Oct 21, 2019) | |||
| 5-81437449-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 5-81442696-T-C | not specified | Uncertain significance (Jun 22, 2023) | ||
| 5-81448792-C-T | not specified | Uncertain significance (Dec 16, 2023) | ||
| 5-81448794-T-A | Malignant tumor of prostate | Uncertain significance (-) | ||
| 5-81461092-C-T | not specified | Uncertain significance (Jan 31, 2024) | ||
| 5-81473705-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
| 5-81473747-T-C | not specified | Uncertain significance (Nov 25, 2024) | ||
| 5-81489293-C-T | not specified | Uncertain significance (Jun 07, 2024) | ||
| 5-81615516-T-C | not specified | Uncertain significance (Nov 07, 2024) | ||
| 5-81636601-G-GT | not specified | Uncertain significance (Nov 07, 2016) | ||
| 5-81650290-A-C | not specified | Uncertain significance (Dec 08, 2021) | ||
| 5-81650311-G-A | not specified | Uncertain significance (Oct 21, 2021) | ||
| 5-81751009-C-T | not specified | Uncertain significance (Aug 12, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SSBP2 | protein_coding | protein_coding | ENST00000320672 | 17 | 338777 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00224 | 125712 | 0 | 2 | 125714 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.45 | 98 | 194 | 0.505 | 0.00000890 | 2332 |
| Missense in Polyphen | 17 | 58.355 | 0.29132 | 737 | ||
| Synonymous | 0.285 | 58 | 60.8 | 0.953 | 0.00000297 | 683 |
| Loss of Function | 4.43 | 2 | 26.7 | 0.0750 | 0.00000130 | 329 |
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 | 0.0000462 | 0.0000462 |
| European (Non-Finnish) | 0.00000900 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.124
Intolerance Scores
- loftool
- 0.112
- rvis_EVS
- -0.03
- rvis_percentile_EVS
- 51.4
Haploinsufficiency Scores
- pHI
- 0.205
- hipred
- Y
- hipred_score
- 0.729
- ghis
- 0.568
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.970
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ssbp2
- Phenotype
- growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); endocrine/exocrine gland phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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); hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); neoplasm; limbs/digits/tail phenotype;
Gene ontology
- Biological process
- regulation of transcription, DNA-templated;positive regulation of transcription by RNA polymerase II
- Cellular component
- nucleus;cytoplasm
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;single-stranded DNA binding