APCS
Basic information
Region (hg38): 1:159587826-159588865
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (29 variants)
- not_provided (2 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the APCS gene is commonly pathogenic or not. These statistics are base on transcript: NM_000001639.4. 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 | 2 | |||||
| missense | 26 | 29 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 26 | 5 | 0 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| APCS | protein_coding | protein_coding | ENST00000255040 | 2 | 1041 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.0317 | 0.621 | 125703 | 0 | 2 | 125705 | 0.00000796 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | -0.233 | 122 | 115 | 1.06 | 0.00000555 | 1441 |
| Missense in Polyphen | 44 | 42.297 | 1.0403 | 590 | ||
| Synonymous | -0.472 | 51 | 46.9 | 1.09 | 0.00000228 | 450 |
| Loss of Function | 0.248 | 2 | 2.42 | 0.828 | 1.02e-7 | 28 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000615 | 0.0000615 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000544 | 0.0000544 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.0000544 | 0.0000544 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Can interact with DNA and histones and may scavenge nuclear material released from damaged circulating cells. May also function as a calcium-dependent lectin.;
- Disease
- DISEASE: Note=SAP is a precursor of amyloid component P which is found in basement membrane and associated with amyloid deposits.;
- Pathway
- Human Complement System;Metabolism of proteins;Amyloid fiber formation
(Consensus)
Recessive Scores
- pRec
- 0.237
Intolerance Scores
- loftool
- 0.914
- rvis_EVS
- -0.05
- rvis_percentile_EVS
- 49.76
Haploinsufficiency Scores
- pHI
- 0.0796
- hipred
- N
- hipred_score
- 0.166
- ghis
- 0.415
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- N
- gene_indispensability_score
- 0.256
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Apcs
- Phenotype
- normal 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); hematopoietic system phenotype; immune system phenotype; renal/urinary system phenotype; homeostasis/metabolism phenotype;
Gene ontology
- Biological process
- negative regulation of acute inflammatory response;protein folding;acute-phase response;complement activation, classical pathway;cellular protein metabolic process;negative regulation by host of viral exo-alpha-sialidase activity;negative regulation by host of viral glycoprotein metabolic process;innate immune response;negative regulation of monocyte differentiation;negative regulation of viral entry into host cell;negative regulation of viral process;chaperone-mediated protein complex assembly;negative regulation of wound healing;negative regulation of exo-alpha-sialidase activity;negative regulation of glycoprotein metabolic process
- Cellular component
- extracellular region;extracellular space;nucleus;collagen-containing extracellular matrix;extracellular exosome;blood microparticle
- Molecular function
- complement component C1q binding;calcium ion binding;low-density lipoprotein particle binding;carbohydrate binding;identical protein binding;virion binding;unfolded protein binding