SCARF1

protein-coding

scavenger receptor class F member 1, the group of Scavenger receptors

Gene summary

The protein encoded by this gene is a scavenger receptor that is expressed in endothelial cells. It regulates the uptake of chemically modified low density lipoproteins, including acetylated low density lipoprotein (Ac-LDL), and it may be involved in atherogenesis. This gene is regulated by the transcription factors ZNF444/EZF-2 and SP1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2013]

MANE transcript

NM_003693.4

Inheritance

—

ClinVar variants

U:138B:14

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.48

Max pathogenic AF

—

Genomic locus

chr17:1,633,858-1,645,744

External References & Databases

Ensembl (ENSG00000074660)

Transcript & Mutation Effects

hg38 • Region Span ~11.9 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 SCARF1 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 145

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_003693.4. 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			1 clinvar	3 clinvar	1 clinvar	5
missense			135 clinvar	9 clinvar	1 clinvar	145
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	138	12	2	152

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_003693.4	RefSeq	NP_003684.2	11	MANE Select
ENST00000263071.9	Ensembl	ENSP00000263071.4	11	MANE Select
NM_145350.3	RefSeq	NP_663325.1	11	Standard
ENST00000434376.6	Ensembl	ENSP00000411167.2	6	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Vesicle-mediated transport
Binding and Uptake of Ligands by Scavenger Receptors
Scavenging by Class F Receptors

Biological Process

cholesterol catabolic process
receptor-mediated endocytosis
cell adhesion
positive regulation of neuron projection development
neuron remodeling

Molecular Function

transmembrane signaling receptor activity
scavenger receptor activity
low-density lipoprotein particle binding

Cellular Component

plasma membrane
integral component of membrane
endocytic vesicle membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000263071
Coding exons: 11
Length: 11890
Individuals with no LoFs: 125586
Homozygous LoFs: 1
Heterozygous LoFs: 157
Defined: 125744
p: 0.000628

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.14	370	437	0.847	0.0000268	5254
Missense (PolyPhen)		92	113.74	0.80887		1398
Synonymous	-1.01	208	190	1.09	0.0000130	1713
Loss of Function	2.80	16	33.5	0.478	0.00000197	381

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00031	0.00031	rare
Latino/Admixed American	0.00049	0.00046	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.0014	0.0012	notable
European (Non-Finnish)	0.0010	0.00084	notable
South Asian	0.00043	0.00042	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). Mediates heterophilic interactions, suggesting a function as adhesion protein. Plays a role in the regulation of neurite-like outgrowth (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0983

Intolerance Scores

LoFtool: 0.869
RVIS EVS: 2.34
RVIS percentile EVS: 98.4

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): H
Indispensability pred.: N
Indispensability score: 0.0443

Gene Damage Prediction

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