APCS
Basic information
Region (hg38): 1:159587826-159588865
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 APCS 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 | 11 | 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 | 11 | 1 | 0 |
Variants in APCS
This is a list of pathogenic ClinVar variants found in the APCS region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
Position | Type | Phenotype | Significance | ClinVar |
---|---|---|---|---|
1-159587931-C-G | not specified | Uncertain significance (Mar 20, 2024) | ||
1-159588140-T-C | not specified | Uncertain significance (Nov 08, 2021) | ||
1-159588158-T-G | not specified | Uncertain significance (Sep 26, 2023) | ||
1-159588167-C-T | not specified | Uncertain significance (Dec 20, 2023) | ||
1-159588169-C-T | Likely benign (Feb 01, 2023) | |||
1-159588211-T-C | not specified | Uncertain significance (Jun 16, 2023) | ||
1-159588256-C-G | not specified | Uncertain significance (Sep 14, 2022) | ||
1-159588308-G-C | not specified | Uncertain significance (Jan 04, 2024) | ||
1-159588367-G-C | not specified | Uncertain significance (Feb 07, 2023) | ||
1-159588373-A-T | not specified | Uncertain significance (Dec 13, 2023) | ||
1-159588374-T-A | not specified | Uncertain significance (Mar 24, 2023) | ||
1-159588437-T-C | not specified | Uncertain significance (Jul 09, 2021) | ||
1-159588464-T-C | not specified | Likely benign (Mar 19, 2024) | ||
1-159588466-G-C | not specified | Uncertain significance (Nov 08, 2022) |
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