SCARF2

protein-coding

scavenger receptor class F member 2, the group of Scavenger receptors

Gene summary

The protein encoded by this gene is similar to SCARF1/SREC-I, a scavenger receptor protein that mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL). This protein has only little activity of internalizing modified low density lipoproteins (LDL), but it can interact with SCARF1 through its extracellular domain. The association of this protein with SCARF1 is suppressed by the presence of scavenger ligands. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]

MANE transcript

NM_182895.5

Inheritance

ClinVar variants

P:14U:167B:58

Top phenotype

Van den Ende-Gupta syndrome

gnomAD constraint

pLI —, LoF o/e 0.06

Max pathogenic AF

—

Genomic locus

chr22:20,424,584-20,437,826

External References & Databases

Ensembl (ENSG00000244486)

Transcript & Mutation Effects

hg38 • Region Span ~13.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

van den Ende-Gupta syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010959

Submitter: Orphanet

van den Ende-Gupta syndromeDEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0010959

Submitter: G2P

van den Ende-Gupta syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010959

Submitter: Labcorp Genetics (formerly Invitae)

van den Ende-Gupta syndromeSTRONG

Inheritance Pattern: AR

Disease ID:MONDO:0010959

Submitter: PanelApp Australia

van den Ende-Gupta syndromeMODERATE

Inheritance Pattern: AR

Disease ID:MONDO:0010959

Submitter: Ambry Genetics

Clinical Genomic Database (CGD)

Van den Ende-Gupta syndromeAR

Manifestation: Craniofacial; Musculoskeletal; Ophthalmologic

Intervention: General

Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing

Refs: 20887961; 23808541; 24478002

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to SCARF2 variants in ClinVar

7 Conditions Cataloged

Inborn genetic diseasesTotal: 145

not providedTotal: 95

Van den Ende-Gupta syndromeTotal: 28

not specifiedTotal: 11

SCARF2-related disorderTotal: 6

Fetal anomalies with a likely genetic causeTotal: 1

MicrocephalyTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_182895.5. 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	34 clinvar	6 clinvar	42
missense	3 clinvar	2 clinvar	158 clinvar	9 clinvar	3 clinvar	175
nonsense	2 clinvar					2
start loss		1 clinvar				1
frameshift	3 clinvar	3 clinvar	2 clinvar		6 clinvar	14
splice donor/acceptor (+/-2bp)			5 clinvar			5
Total	8	6	167	43	15	239

Highest pathogenic variant AF is 0.000017121365

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 33 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_182895.5	RefSeq	NP_878315.2	11	MANE Select
ENST00000622235.5	Ensembl	ENSP00000477564.2	11	MANE Select
NM_153334.7	RefSeq	NP_699165.3	11	Standard
ENST00000623402.1	Ensembl	ENSP00000485276.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules

Molecular Function

protein binding

Cellular Component

focal adhesion
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000266214
Coding exons: 11
Length: 13273
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 47
Defined: 125734
p: 0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	3.02	305	494	0.618	0.0000336	5321
Missense (PolyPhen)		107	230.93	0.46334		2493
Synonymous	2.55	182	231	0.787	0.0000186	1787
Loss of Function	5.01	2	33.1	0.0604	0.00000158	361

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0024	0.0021	notable
Finnish	0	0.0	absent
European (Non-Finnish)	0.000041	0.000035	rare
South Asian	0	0.0	absent
Other	0.00017	0.00016	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable adhesion protein, which mediates homophilic and heterophilic interactions. In contrast to SCARF1, it poorly mediates the binding and degradation of acetylated low density lipoprotein (Ac-LDL) (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.145

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.226

Gene Damage Prediction

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