SERF2
Basic information
Region (hg38): 15:43777086-43804427
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 SERF2 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 | 7 | 0 | 0 |
Variants in SERF2
This is a list of pathogenic ClinVar variants found in the SERF2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
15-43793647-C-G | not specified | Uncertain significance (Mar 13, 2023) | ||
15-43793767-C-T | not specified | Uncertain significance (May 04, 2022) | ||
15-43793809-C-T | not specified | Uncertain significance (Nov 21, 2023) | ||
15-43793815-T-C | not specified | Uncertain significance (Dec 27, 2023) | ||
15-43793821-G-C | not specified | Uncertain significance (Oct 06, 2021) | ||
15-43793823-G-A | not specified | Uncertain significance (Oct 06, 2022) | ||
15-43793946-C-A | not specified | Uncertain significance (Dec 28, 2022) | ||
15-43800605-C-T | not specified | Uncertain significance (Nov 17, 2022) | ||
15-43800606-G-A | not specified | Uncertain significance (Nov 10, 2022) | ||
15-43800612-G-A | not specified | Uncertain significance (Sep 22, 2023) | ||
15-43800634-G-C | not specified | Uncertain significance (Apr 26, 2023) | ||
15-43800635-G-A | not specified | Uncertain significance (Jun 02, 2023) | ||
15-43800641-G-A | not specified | Uncertain significance (Oct 13, 2023) | ||
15-43800658-G-A | Benign (May 16, 2018) | |||
15-43800666-C-T | not specified | Uncertain significance (Dec 15, 2022) | ||
15-43801560-G-A | Benign (May 16, 2018) | |||
15-43801711-A-G | not specified | Uncertain significance (Aug 16, 2022) | ||
15-43801716-T-C | Benign (May 16, 2018) | |||
15-43801735-G-A | not specified | Uncertain significance (May 21, 2024) | ||
15-43801793-C-T | not specified | Uncertain significance (May 30, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
SERF2 | protein_coding | protein_coding | ENST00000409960 | 3 | 25503 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0232 | 0.783 | 125725 | 0 | 22 | 125747 | 0.0000875 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.227 | 95 | 101 | 0.937 | 0.00000536 | 1078 |
Missense in Polyphen | 3 | 7.278 | 0.4122 | 72 | ||
Synonymous | 0.919 | 34 | 41.5 | 0.819 | 0.00000246 | 376 |
Loss of Function | 0.947 | 3 | 5.37 | 0.559 | 2.40e-7 | 63 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000243 | 0.000242 |
Ashkenazi Jewish | 0.00 | 0.00 |
East Asian | 0.00 | 0.00 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.0000265 | 0.0000264 |
Middle Eastern | 0.00 | 0.00 |
South Asian | 0.000425 | 0.000425 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
Recessive Scores
- pRec
- 0.113
Haploinsufficiency Scores
- pHI
- 0.242
- hipred
- N
- hipred_score
- 0.146
- ghis
- 0.504
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.764
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Serf2
- Phenotype
Gene ontology
- Biological process
- biological_process
- Cellular component
- nucleus;cytosol
- Molecular function
- molecular_function