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GeneBe

SAA2

serum amyloid A2

Basic information

Region (hg38): 11:18239222-18248668

Links

ENSG00000134339NCBI:6289OMIM:104751HGNC:10514Uniprot:P0DJI9AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAA2 gene.

  • Inborn genetic diseases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAA2 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
0
missense
1
clinvar
1
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 1 0 0

Variants in SAA2

This is a list of pathogenic ClinVar variants found in the SAA2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
11-18245418-G-A not specified Uncertain significance (Jun 21, 2023)2596057

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAA2protein_codingprotein_codingENST00000526900 39421
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.000002700.09751257050271257320.000107
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.1167471.31.040.00000403778
Missense in Polyphen2726.3861.0233324
Synonymous0.2132728.40.9490.00000176237
Loss of Function-1.1774.361.612.70e-744

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0002400.000239
Ashkenazi Jewish0.000.00
East Asian0.0003260.000326
Finnish0.00004780.0000462
European (Non-Finnish)0.00009700.0000967
Middle Eastern0.0003260.000326
South Asian0.00006540.0000653
Other0.0001640.000163

dbNSFP

Source: dbNSFP

Function
FUNCTION: Major acute phase reactant. Apolipoprotein of the HDL complex.;
Disease
DISEASE: Note=Reactive, secondary amyloidosis is characterized by the extracellular accumulation in various tissues of the SAA2 protein. These deposits are highly insoluble and resistant to proteolysis; they disrupt tissue structure and compromise function. {ECO:0000269|PubMed:1463770}.;
Pathway
Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism;Endogenous TLR signaling (Consensus)

Recessive Scores

pRec
0.194

Intolerance Scores

loftool
0.844
rvis_EVS
0.73
rvis_percentile_EVS
85.98

Haploinsufficiency Scores

pHI
0.195
hipred
N
hipred_score
0.172
ghis
0.431

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.538

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
acute-phase response;positive chemotaxis;cell chemotaxis
Cellular component
extracellular space;high-density lipoprotein particle;extracellular exosome
Molecular function
chemoattractant activity