SCARA3

protein-coding

scavenger receptor class A member 3, the group of MicroRNA protein coding host genes|Scavenger receptors

Gene summary

This gene encodes a macrophage scavenger receptor-like protein. This protein has been shown to deplete reactive oxygen species, and thus play an important role in protecting cells from oxidative stress. The expression of this gene is induced by oxidative stress. Alternatively spliced transcript variants encoding distinct isoforms have been described. [provided by RefSeq, Jul 2008]

MANE transcript

NM_016240.3

Inheritance

—

ClinVar variants

U:95B:10

Top phenotype

SCARA3-related disorder

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr8:27,633,868-27,676,776

External References & Databases

Ensembl (ENSG00000168077)

Transcript & Mutation Effects

hg38 • Region Span ~42.9 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCARA3 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 100

SCARA3-related disorderTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_016240.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	2 clinvar		4
missense			90 clinvar	8 clinvar		98
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	95	10	0	105

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_016240.3	RefSeq	NP_057324.2	6	MANE Select
ENST00000301904.4	Ensembl	ENSP00000301904.3	6	MANE Select
NM_182826.2	RefSeq	NP_878185.1	6	Standard
ENST00000337221.8	Ensembl	ENSP00000337985.3	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

complement activation, lectin pathway
growth plate cartilage chondrocyte morphogenesis
receptor-mediated endocytosis
response to oxidative stress
UV protection

Molecular Function

scavenger receptor activity
calcium ion binding
protein binding
mannose binding

Cellular Component

Golgi membrane
collagen trimer
extracellular space
endoplasmic reticulum
endoplasmic reticulum membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000301904
Coding exons: 6
Length: 42909
Individuals with no LoFs: 125682
Homozygous LoFs: 0
Heterozygous LoFs: 66
Defined: 125748
p: 0.000262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.253	333	346	0.962	0.0000209	3880
Missense (PolyPhen)		113	120.56	0.9373		1323
Synonymous	-1.22	174	155	1.13	0.0000104	1291
Loss of Function	1.40	15	22.1	0.679	0.00000118	240

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00032	0.00031	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0.0022	0.0022	notable
East Asian	0.00011	0.00011	rare
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.00011	0.00011	rare
South Asian	0.00036	0.00036	rare
Other	0.00016	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Seems to protect cells by scavenging oxidative molecules or harmful products of oxidation. {ECO:0000269|PubMed:9580669}.;

Recessive Scores

pRec: 0.143

Intolerance Scores

LoFtool: 0.130
RVIS EVS: -1.22
RVIS percentile EVS: 5.64

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.272

Gene Damage Prediction

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