APCS

amyloid P component, serum, the group of Short pentraxins

Basic information

Region (hg38): 1:159587826-159588865

Links

ENSG00000132703NCBI:325OMIM:104770HGNC:584Uniprot:P02743AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the APCS gene.

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
clinvar
1
missense
11
clinvar
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)3306454
1-159588140-T-C not specified Uncertain significance (Nov 08, 2021)2259349
1-159588158-T-G not specified Uncertain significance (Sep 26, 2023)3127794
1-159588167-C-T not specified Uncertain significance (Dec 20, 2023)3127795
1-159588169-C-T Likely benign (Feb 01, 2023)2639484
1-159588211-T-C not specified Uncertain significance (Jun 16, 2023)2602791
1-159588256-C-G not specified Uncertain significance (Sep 14, 2022)2311777
1-159588308-G-C not specified Uncertain significance (Jan 04, 2024)3127796
1-159588367-G-C not specified Uncertain significance (Feb 07, 2023)2481752
1-159588373-A-T not specified Uncertain significance (Dec 13, 2023)3127797
1-159588374-T-A not specified Uncertain significance (Mar 24, 2023)2570518
1-159588437-T-C not specified Uncertain significance (Jul 09, 2021)2307609
1-159588464-T-C not specified Likely benign (Mar 19, 2024)3306444
1-159588466-G-C not specified Uncertain significance (Nov 08, 2022)2323792

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
APCSprotein_codingprotein_codingENST00000255040 21041
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.03170.621125703021257050.00000796
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2331221151.060.000005551441
Missense in Polyphen4442.2971.0403590
Synonymous-0.4725146.91.090.00000228450
Loss of Function0.24822.420.8281.02e-728

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.00006150.0000615
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.000.00
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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