SYF2
Basic information
Region (hg38): 1:25222275-25232502
Previous symbols: [ "CBPIN" ]
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 SYF2 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 | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 6 | 1 | 0 |
Variants in SYF2
This is a list of pathogenic ClinVar variants found in the SYF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-25223393-T-C | not specified | Uncertain significance (Jan 08, 2024) | ||
| 1-25225048-G-T | not specified | Uncertain significance (Mar 07, 2024) | ||
| 1-25227464-A-G | not specified | Uncertain significance (Mar 02, 2023) | ||
| 1-25227478-G-A | not specified | Uncertain significance (Jan 09, 2024) | ||
| 1-25232106-G-C | not specified | Uncertain significance (Jul 13, 2021) | ||
| 1-25232150-T-A | not specified | Uncertain significance (Jun 22, 2024) | ||
| 1-25232174-G-T | not specified | Uncertain significance (Mar 07, 2023) | ||
| 1-25232199-T-C | not specified | Likely benign (Feb 12, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SYF2 | protein_coding | protein_coding | ENST00000236273 | 7 | 9824 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00561 | 0.973 | 125724 | 0 | 22 | 125746 | 0.0000875 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 0.257 | 128 | 136 | 0.938 | 0.00000698 | 1598 |
| Missense in Polyphen | 21 | 35.846 | 0.58585 | 387 | ||
| Synonymous | -0.959 | 56 | 47.6 | 1.18 | 0.00000226 | 429 |
| Loss of Function | 2.02 | 6 | 14.2 | 0.422 | 6.95e-7 | 187 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.000261 | 0.000261 |
| Ashkenazi Jewish | 0.000103 | 0.0000992 |
| East Asian | 0.0000545 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000617 | 0.0000615 |
| Middle Eastern | 0.0000545 | 0.0000544 |
| South Asian | 0.0000985 | 0.0000980 |
| Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in pre-mRNA splicing as component of the spliceosome (PubMed:11991638, PubMed:28502770, PubMed:28076346). {ECO:0000269|PubMed:11991638, ECO:0000269|PubMed:28076346, ECO:0000269|PubMed:28502770}.;
- Pathway
- Spliceosome - Homo sapiens (human);Metabolism of RNA;mRNA Splicing - Major Pathway;mRNA Splicing;Processing of Capped Intron-Containing Pre-mRNA
(Consensus)
Recessive Scores
- pRec
- 0.0702
Intolerance Scores
- loftool
- 0.804
- rvis_EVS
- 0.42
- rvis_percentile_EVS
- 76.81
Haploinsufficiency Scores
- pHI
- 0.239
- hipred
- Y
- hipred_score
- 0.723
- ghis
- 0.408
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.889
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Syf2
- 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); embryo phenotype; cellular phenotype;
Zebrafish Information Network
- Gene name
- syf2
- Affected structure
- neuron
- Phenotype tag
- abnormal
- Phenotype quality
- decreased amount
Gene ontology
- Biological process
- mRNA splicing, via spliceosome;in utero embryonic development;mitotic G2 DNA damage checkpoint;gastrulation;positive regulation of cell population proliferation;embryonic organ development
- Cellular component
- Prp19 complex;nucleus;nucleoplasm;nuclear speck;U2-type catalytic step 2 spliceosome;catalytic step 2 spliceosome;post-mRNA release spliceosomal complex
- Molecular function
- RNA binding;protein binding