SSBP3
single stranded DNA binding protein 3, the group of Wnt enhanceosome complex
Basic information
Region (hg38): 1:54225432-54413479
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (10 variants)
- not provided (1 variants)
- Developmental disorder (1 variants)
- Neurodevelopmental disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SSBP3 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 | 1 | |||||
| missense | 10 | 10 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 2 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 12 | 1 | 0 |
Variants in SSBP3
This is a list of pathogenic ClinVar variants found in the SSBP3 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-54228299-C-T | not specified | Uncertain significance (Jan 04, 2024) | ||
| 1-54228773-C-G | not specified | Uncertain significance (Mar 28, 2023) | ||
| 1-54228816-C-G | not specified | Uncertain significance (Nov 18, 2022) | ||
| 1-54239176-T-C | not specified | Uncertain significance (May 15, 2024) | ||
| 1-54240909-G-A | Likely benign (Jul 01, 2022) | |||
| 1-54242199-C-CA | Developmental disorder | Uncertain significance (Jan 13, 2022) | ||
| 1-54242207-G-A | not specified | Uncertain significance (Nov 30, 2021) | ||
| 1-54243284-T-C | not specified | Uncertain significance (Jan 09, 2024) | ||
| 1-54243287-C-T | not specified | Uncertain significance (Jul 20, 2022) | ||
| 1-54251844-G-A | not specified | Uncertain significance (Feb 10, 2022) | ||
| 1-54257146-G-A | not specified | Uncertain significance (Feb 05, 2024) | ||
| 1-54257149-G-A | not specified | Uncertain significance (Jun 09, 2022) | ||
| 1-54257165-C-T | not specified | Uncertain significance (Dec 26, 2023) | ||
| 1-54258109-G-A | not specified | Uncertain significance (Feb 06, 2023) | ||
| 1-54281481-T-C | not specified | Uncertain significance (Apr 07, 2022) | ||
| 1-54404589-GC-G | Neurodevelopmental disorder | Uncertain significance (Jul 13, 2021) | ||
| 1-54404878-C-T | not specified | Uncertain significance (Dec 28, 2023) | ||
| 1-54406001-G-A | not specified | Uncertain significance (Jan 26, 2022) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SSBP3 | protein_coding | protein_coding | ENST00000371320 | 18 | 188048 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000321 | 125722 | 0 | 2 | 125724 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.75 | 117 | 236 | 0.496 | 0.0000133 | 2502 |
| Missense in Polyphen | 41 | 88.829 | 0.46156 | 929 | ||
| Synonymous | -1.32 | 112 | 95.6 | 1.17 | 0.00000733 | 745 |
| Loss of Function | 4.90 | 2 | 31.9 | 0.0627 | 0.00000180 | 331 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000104 | 0.00000879 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: May be involved in transcription regulation of the alpha 2(I) collagen gene where it binds to the single-stranded polypyrimidine sequences in the promoter region. {ECO:0000250}.;
Recessive Scores
- pRec
- 0.0839
Intolerance Scores
- loftool
- rvis_EVS
- -0.65
- rvis_percentile_EVS
- 16.36
Haploinsufficiency Scores
- pHI
- 0.155
- hipred
- Y
- hipred_score
- 0.749
- ghis
- 0.591
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- K
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.966
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ssbp3
- Phenotype
- cellular phenotype; craniofacial phenotype; growth/size/body region phenotype; embryo phenotype; skeleton phenotype; limbs/digits/tail phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); normal 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);
Zebrafish Information Network
- Gene name
- ssbp3a
- Affected structure
- Rohon-Beard neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- hematopoietic progenitor cell differentiation;positive regulation of cell population proliferation;prechordal plate formation;midbrain-hindbrain boundary initiation;positive regulation of transcription by RNA polymerase II;head development;head morphogenesis;protein-containing complex assembly;positive regulation of anterior head development
- Cellular component
- nucleus;protein-containing complex
- Molecular function
- RNA polymerase II proximal promoter sequence-specific DNA binding;single-stranded DNA binding;protein binding