TFCP2L1
transcription factor CP2 like 1
Basic information
Region (hg38): 2:121216587-121285202
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (41 variants)
- not_provided (4 variants)
- Chronic_kidney_disease (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the TFCP2L1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014553.3. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | |||||
| missense | 41 | 42 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 41 | 0 | 3 |
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| TFCP2L1 | protein_coding | protein_coding | ENST00000263707 | 15 | 68621 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.0000381 | 125741 | 0 | 2 | 125743 | 0.00000795 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.63 | 213 | 291 | 0.731 | 0.0000181 | 3130 |
| Missense in Polyphen | 66 | 121.4 | 0.54368 | 1273 | ||
| Synonymous | 0.418 | 119 | 125 | 0.952 | 0.00000836 | 904 |
| Loss of Function | 5.18 | 1 | 33.2 | 0.0302 | 0.00000191 | 333 |
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) | 0.00000880 | 0.00000879 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000327 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that facilitates establishment and maintenance of pluripotency in embryonic stem cells (ESCs) (PubMed:25215486, PubMed:26906118). With KLF2, acts as the major effector of self-renewal that mediates induction of pluripotency downstream of LIF/STAT3 and Wnt/beta-catenin signaling (By similarity). Required for normal duct development in the salivary gland and kidney (By similarity). Coordinates the development of the kidney collecting ducts intercalated (IC) and principal (PC) cells, which regulate acid-base and salt-water homeostasis, respectively (By similarity). Regulates the expression of IC genes including subunits B1 and D2 of the V-ATPase complex, OXGR1, CA12, SLC4A1, AQP6 and IC-specific transcription factor FOXI1 (By similarity). Regulates also the expression of JAG1 and subsequent notch signaling in the collecting duct (By similarity). JAG1 initiates notch signaling in PCs but inhibits notch signaling in ICs (By similarity). Acts as a transcriptional suppressor that may suppress UBP1-mediated transcriptional activation (By similarity). Modulates the placental expression of CYP11A1 (PubMed:10644752). {ECO:0000250|UniProtKB:Q3UNW5, ECO:0000269|PubMed:10644752, ECO:0000269|PubMed:25215486, ECO:0000269|PubMed:26906118}.;
Recessive Scores
- pRec
- 0.104
Intolerance Scores
- loftool
- 0.0581
- rvis_EVS
- -0.4
- rvis_percentile_EVS
- 26.85
Haploinsufficiency Scores
- pHI
- 0.130
- hipred
- Y
- hipred_score
- 0.768
- ghis
- 0.508
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.575
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Tfcp2l1
- Phenotype
- endocrine/exocrine gland phenotype; growth/size/body region phenotype; homeostasis/metabolism phenotype; craniofacial phenotype; digestive/alimentary 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); respiratory system phenotype; renal/urinary system phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;cell morphogenesis;epithelial cell maturation;regulation of transcription by RNA polymerase II;steroid biosynthetic process;cytoplasm organization;salivary gland development;female pregnancy;determination of adult lifespan;positive regulation of growth
- Cellular component
- fibrillar center;nucleus;mitochondrion;membrane
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription factor activity;transcription corepressor activity;sequence-specific DNA binding