SAA2

serum amyloid A2

Basic information

Region (hg38): 11:18239222-18248668

Links

ENSG00000134339 ∙ NCBI:6289 ∙ OMIM:104751 ∙ HGNC:10514 ∙ Uniprot:P0DJI9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

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.

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 variant						0
non coding						0
Total	0	0	0	0	0

Variants in SAA2

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

Position	Type	Phenotype	Significance	ClinVar
11-18245418-G-A		Inborn genetic diseases	Uncertain significance (Jun 21, 2023)

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_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