FERD3L
Basic information
Region (hg38): 7:19144782-19145421
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 FERD3L 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 | 10 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 10 | 1 | 0 |
Variants in FERD3L
This is a list of pathogenic ClinVar variants found in the FERD3L region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 7-19144878-T-A | not specified | Uncertain significance (Aug 27, 2024) | ||
| 7-19144900-C-G | not specified | Uncertain significance (Feb 05, 2025) | ||
| 7-19144936-G-A | not specified | Uncertain significance (May 13, 2024) | ||
| 7-19144947-C-T | not specified | Uncertain significance (May 05, 2023) | ||
| 7-19144957-T-C | not specified | Uncertain significance (Nov 09, 2024) | ||
| 7-19144974-G-C | not specified | Uncertain significance (Jan 22, 2024) | ||
| 7-19145009-G-C | not specified | Uncertain significance (Aug 20, 2023) | ||
| 7-19145016-T-C | not specified | Uncertain significance (Apr 12, 2024) | ||
| 7-19145176-C-T | not specified | Uncertain significance (Apr 25, 2022) | ||
| 7-19145229-G-A | not specified | Likely benign (Feb 27, 2024) | ||
| 7-19145244-C-T | not specified | Uncertain significance (Sep 25, 2024) | ||
| 7-19145257-C-T | not specified | Uncertain significance (Sep 01, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FERD3L | protein_coding | protein_coding | ENST00000275461 | 1 | 640 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.319 | 0.619 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.405 | 110 | 98.7 | 1.11 | 0.00000436 | 1071 |
| Missense in Polyphen | 32 | 33.733 | 0.94864 | 347 | ||
| Synonymous | -2.30 | 63 | 43.7 | 1.44 | 0.00000198 | 345 |
| Loss of Function | 1.44 | 1 | 4.18 | 0.239 | 1.83e-7 | 47 |
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) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Transcription factor that binds to the E-box and functions as inhibitor of transcription. DNA binding requires dimerization with an E protein. Inhibits transcription activation by ASCL1/MASH1 by sequestering E proteins (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.105
Intolerance Scores
- loftool
- 0.185
- rvis_EVS
- -0.19
- rvis_percentile_EVS
- 39.68
Haploinsufficiency Scores
- pHI
- 0.0690
- hipred
- Y
- hipred_score
- 0.506
- ghis
- 0.527
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.438
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ferd3l
- Phenotype
- embryo 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); cellular phenotype;
Gene ontology
- Biological process
- negative regulation of transcription by RNA polymerase II;floor plate development;negative regulation of transcription, DNA-templated;cell development;regulation of neurogenesis
- Cellular component
- nucleus
- Molecular function
- RNA polymerase II regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;DNA-binding transcription repressor activity, RNA polymerase II-specific;protein binding;protein dimerization activity