SCFD1
Basic information
Region (hg38): 14:30622291-30737694
Previous symbols: [ "C14orf163" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (63 variants)
- not_provided (3 variants)
- Amyotrophic_lateral_sclerosis (2 variants)
- SCFD1-related_disorder (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCFD1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016106.4. 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 | 1 | |||||
| missense | 68 | 69 | ||||
| nonsense | 2 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 11 | 11 | ||||
| Total | 0 | 0 | 82 | 1 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| SCFD1 | protein_coding | protein_coding | ENST00000458591 | 25 | 113701 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.000382 | 125722 | 0 | 10 | 125732 | 0.0000398 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.05 | 225 | 330 | 0.682 | 0.0000155 | 4207 |
| Missense in Polyphen | 61 | 107.11 | 0.56951 | 1425 | ||
| Synonymous | -0.149 | 110 | 108 | 1.02 | 0.00000526 | 1152 |
| Loss of Function | 5.50 | 5 | 44.6 | 0.112 | 0.00000231 | 551 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000742 | 0.0000742 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.0000467 | 0.0000462 |
| European (Non-Finnish) | 0.0000537 | 0.0000528 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.0000328 | 0.0000327 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Plays a role in SNARE-pin assembly and Golgi-to-ER retrograde transport via its interaction with COG4. Involved in vesicular transport between the endoplasmic reticulum and the Golgi (By similarity). {ECO:0000250}.;
- Pathway
- Vesicle-mediated transport;Membrane Trafficking;Post-translational protein modification;Metabolism of proteins;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPII-mediated vesicle transport;ER to Golgi Anterograde Transport
(Consensus)
Recessive Scores
- pRec
- 0.118
Intolerance Scores
- loftool
- 0.511
- rvis_EVS
- -0.18
- rvis_percentile_EVS
- 40.36
Haploinsufficiency Scores
- pHI
- 0.227
- hipred
- N
- hipred_score
- 0.488
- ghis
- 0.655
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- E
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.981
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Scfd1
- Phenotype
Zebrafish Information Network
- Gene name
- scfd1
- Affected structure
- goblet cell
- Phenotype tag
- abnormal
- Phenotype quality
- absent
Gene ontology
- Biological process
- cell morphogenesis;response to hypoxia;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;post-Golgi vesicle-mediated transport;vesicle docking involved in exocytosis;response to toxic substance;protein transport;COPII vesicle coating;regulation of protein transport;regulation of ER to Golgi vesicle-mediated transport;toxin transport;negative regulation of autophagosome assembly
- Cellular component
- endoplasmic reticulum membrane;Golgi-associated vesicle;cis-Golgi network;cytosol;plasma membrane;Golgi cisterna membrane
- Molecular function
- protein binding;syntaxin binding;protein-containing complex binding;protein N-terminus binding