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GeneBe

SAA4

serum amyloid A4, constitutive

Basic information

Region (hg38): 11:18231354-18236802

Links

ENSG00000148965NCBI:6291OMIM:104752HGNC:10516Uniprot:P35542AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SAA4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SAA4 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
0
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
?
0
non coding
?
0
Total 0 0 0 0 0

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
SAA4protein_codingprotein_codingENST00000278222 35545
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.01230.6651257260101257360.0000398
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-0.2958476.71.090.00000413847
Missense in Polyphen2223.7610.9259290
Synonymous0.8392227.60.7970.00000161240
Loss of Function0.51134.120.7281.74e-748

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.0004350.000435
Finnish0.000.00
European (Non-Finnish)0.000008790.00000879
Middle Eastern0.0004350.000435
South Asian0.00003270.0000327
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Major acute phase reactant. Apolipoprotein of the HDL complex.;
Pathway
Selenium Micronutrient Network;Vitamin B12 Metabolism;Folate Metabolism (Consensus)

Recessive Scores

pRec
0.195

Intolerance Scores

loftool
0.535
rvis_EVS
0.66
rvis_percentile_EVS
84.35

Haploinsufficiency Scores

pHI
0.0313
hipred
N
hipred_score
0.112
ghis
0.414

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
E
gene_indispensability_score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Saa4
Phenotype

Gene ontology

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