SAA2

serum amyloid A2

Basic information

Region (hg38): 11:18239223-18248668

Links

ENSG00000134339

∙ NCBI:6289 ∙ OMIM:104751 ∙ HGNC:10514 ∙ Uniprot:P0DJI9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

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

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

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SAA2	protein_coding	protein_coding	ENST00000526900	3	9421

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000270	0.0975	125705	0	27	125732	0.000107

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.116	74	71.3	1.04	0.00000403	778
Missense in Polyphen		27	26.386	1.0233		324
Synonymous	0.213	27	28.4	0.949	0.00000176	237
Loss of Function	-1.17	7	4.36	1.61	2.70e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000240	0.000239
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.0000478	0.0000462
European (Non-Finnish)	0.0000970	0.0000967
Middle Eastern	0.000326	0.000326
South Asian	0.0000654	0.0000653
Other	0.000164	0.000163

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

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

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