FICD
Basic information
Region (hg38): 12:108515276-108525837
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- Inborn genetic diseases (27 variants)
- not provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FICD 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 | 1 | |||||
missense | 27 | 28 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 27 | 0 | 2 |
Variants in FICD
This is a list of pathogenic ClinVar variants found in the FICD region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
12-108516986-C-T | not specified | Uncertain significance (Jun 22, 2021) | ||
12-108517038-C-G | not specified | Uncertain significance (Oct 25, 2023) | ||
12-108517040-G-A | not specified | Uncertain significance (Mar 01, 2024) | ||
12-108517055-C-T | not specified | Likely benign (Sep 26, 2023) | ||
12-108517078-T-G | not specified | Uncertain significance (Oct 03, 2022) | ||
12-108517160-G-A | not specified | Uncertain significance (Jan 10, 2023) | ||
12-108518417-A-G | not specified | Uncertain significance (Jun 07, 2023) | ||
12-108518516-G-A | not specified | Uncertain significance (Oct 12, 2022) | ||
12-108518522-G-A | not specified | Uncertain significance (Mar 29, 2023) | ||
12-108518523-C-T | not specified | Uncertain significance (May 03, 2023) | ||
12-108518528-A-G | not specified | Uncertain significance (Apr 05, 2023) | ||
12-108518547-C-G | not specified | Uncertain significance (Nov 08, 2022) | ||
12-108518547-C-T | not specified | Uncertain significance (Apr 05, 2023) | ||
12-108518574-C-T | not specified | Uncertain significance (Mar 01, 2024) | ||
12-108518612-T-C | not specified | Uncertain significance (Dec 22, 2023) | ||
12-108518622-A-C | Benign (Jun 26, 2018) | |||
12-108518669-G-A | not specified | Uncertain significance (Oct 29, 2021) | ||
12-108518766-A-G | not specified | Uncertain significance (Nov 10, 2022) | ||
12-108518778-T-C | not specified | Uncertain significance (Jun 01, 2023) | ||
12-108518844-C-A | not specified | Uncertain significance (Dec 01, 2022) | ||
12-108518852-G-A | not specified | Uncertain significance (Jul 14, 2021) | ||
12-108518858-C-A | not specified | Uncertain significance (May 02, 2023) | ||
12-108518937-C-G | not specified | Uncertain significance (Nov 23, 2021) | ||
12-108518937-C-T | not specified | Uncertain significance (Aug 16, 2021) | ||
12-108518939-C-T | not specified | Uncertain significance (Jan 03, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
FICD | protein_coding | protein_coding | ENST00000552695 | 2 | 10653 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
0.0102 | 0.949 | 125715 | 0 | 33 | 125748 | 0.000131 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | 0.315 | 278 | 293 | 0.948 | 0.0000192 | 2982 |
Missense in Polyphen | 102 | 109.82 | 0.92882 | 1057 | ||
Synonymous | -0.881 | 147 | 134 | 1.10 | 0.0000101 | 953 |
Loss of Function | 1.77 | 5 | 11.5 | 0.436 | 4.90e-7 | 148 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 0.000606 | 0.000604 |
Ashkenazi Jewish | 0.0000992 | 0.0000992 |
East Asian | 0.0000544 | 0.0000544 |
Finnish | 0.00 | 0.00 |
European (Non-Finnish) | 0.000124 | 0.000123 |
Middle Eastern | 0.0000544 | 0.0000544 |
South Asian | 0.000106 | 0.0000980 |
Other | 0.000163 | 0.000163 |
dbNSFP
Source:
- Function
- FUNCTION: Protein that can both mediate the addition of adenosine 5'-monophosphate (AMP) to specific residues of target proteins (AMPylation), and the removal of the same modification from target proteins (de-AMPylation), depending on the context (By similarity). The side chain of Glu-231 determines which of the two opposing activities (AMPylase or de-AMPylase) will take place (By similarity). Acts as a key regulator of the ERN1/IRE1-mediated unfolded protein response (UPR) by mediating AMPylation or de- AMPylation of HSPA5/BiP (PubMed:25601083). In unstressed cells, acts as an adenylyltransferase by mediating AMPylation of HSPA5/BiP at 'Thr-518', thereby inactivating it (By similarity). In response to endoplasmic reticulum stress, acts as a phosphodiesterase by mediating removal of ATP (de-AMPylation) from HSPA5/BiP at 'Thr-518', leading to restore HSPA5/BiP activity (By similarity). Although it is able to AMPylate RhoA, Rac and Cdc42 Rho GTPases in vitro, Rho GTPases do not constitute physiological substrates (PubMed:19362538, PubMed:25601083). {ECO:0000250|UniProtKB:A0A061I403, ECO:0000269|PubMed:22266942, ECO:0000269|PubMed:25435325, ECO:0000269|PubMed:25601083, ECO:0000305|PubMed:19362538}.;
Recessive Scores
- pRec
- 0.119
Intolerance Scores
- loftool
- 0.187
- rvis_EVS
- -0.84
- rvis_percentile_EVS
- 11.36
Haploinsufficiency Scores
- pHI
- 0.164
- hipred
- N
- hipred_score
- 0.325
- ghis
- 0.560
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.931
Gene Damage Prediction
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | Medium | Medium | Medium |
Primary Immunodeficiency | Medium | Medium | Medium |
Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ficd
- Phenotype
Gene ontology
- Biological process
- response to unfolded protein;protein adenylylation;negative regulation of GTPase activity;response to endoplasmic reticulum stress;protein deadenylylation;regulation of IRE1-mediated unfolded protein response
- Cellular component
- integral component of endoplasmic reticulum membrane
- Molecular function
- ATP binding;Hsp70 protein binding;identical protein binding;protein homodimerization activity;protein adenylylhydrolase activity;chaperone binding;protein adenylyltransferase activity