SCARF2

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

Basic information

Region (hg38): 22:20424583-20437826

Links

ENSG00000244486 ∙ ∙ OMIM:613619 ∙ HGNC:19869 ∙ Uniprot:Q96GP6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• van den Ende-Gupta syndrome (Definitive), mode of inheritance: AR
• van den Ende-Gupta syndrome (Limited), mode of inheritance: AR
• van den Ende-Gupta syndrome (Supportive), mode of inheritance: AR
• van den Ende-Gupta syndrome (Moderate), mode of inheritance: AR
• van den Ende-Gupta syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Van den Ende-Gupta syndrome	AR	General	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	Craniofacial; Musculoskeletal; Ophthalmologic	20887961; 23808541; 24478002

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SCARF2 gene.

• Van den Ende-Gupta syndrome (3 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SCARF2 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				17	6	23
missense		2	85	6	6	99
nonsense	1					1
start loss		1				1
frameshift	2				6	8
inframe indel			2			2
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding				9	21	30
Total	3	3	87	32	39

Highest pathogenic variant AF is 0.0000801

Variants in SCARF2

This is a list of pathogenic ClinVar variants found in the SCARF2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
22-20425388-G-A		Inborn genetic diseases	Uncertain significance (Jun 16, 2023)
22-20425397-C-T		Inborn genetic diseases	Uncertain significance (Apr 19, 2024)
22-20425400-C-T		Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
22-20425401-C-T		Inborn genetic diseases	Uncertain significance (Feb 06, 2023)
22-20425414-C-T			Likely benign (Jul 01, 2023)
22-20425416-C-T			Uncertain significance (Aug 01, 2022)
22-20425418-T-C		Inborn genetic diseases	Uncertain significance (Mar 31, 2024)
22-20425421-C-A		Inborn genetic diseases	Uncertain significance (Jun 22, 2023)
22-20425421-C-T			Uncertain significance (Apr 08, 2022)
22-20425430-T-C		Inborn genetic diseases	Uncertain significance (Jan 17, 2024)
22-20425438-C-T			Likely benign (Nov 03, 2023)
22-20425444-CT-C		Van den Ende-Gupta syndrome	Pathogenic (May 01, 2014)
22-20425454-G-A		not specified	Conflicting classifications of pathogenicity (Dec 13, 2023)
22-20425463-C-T		Inborn genetic diseases	Uncertain significance (Aug 10, 2021)
22-20425478-G-C		Van den Ende-Gupta syndrome	Benign (Jan 31, 2024)
22-20425488-C-T		not specified • Inborn genetic diseases	Uncertain significance (Apr 25, 2023)
22-20425532-G-C		Van den Ende-Gupta syndrome • not specified	Benign (Jan 31, 2024)
22-20425539-C-T		Inborn genetic diseases	Uncertain significance (Aug 02, 2023)
22-20425548-C-T		Inborn genetic diseases	Uncertain significance (Apr 01, 2024)
22-20425635-G-A			Likely benign (Sep 08, 2023)
22-20425649-C-T		Inborn genetic diseases	Likely benign (Feb 15, 2023)
22-20425656-G-G		not specified	Benign (-)
22-20425656-GC-GC			Benign (Jan 31, 2024)
22-20425683-C-CG		not specified	Benign (Jan 31, 2024)
22-20425688-G-GC		Van den Ende-Gupta syndrome	Benign (Jul 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SCARF2	protein_coding	protein_coding	ENST00000266214	11	13273

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000202	125687	0	47	125734	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.02	305	494	0.618	0.0000336	5321
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000152
Ashkenazi Jewish	0.00	0.00
East Asian	0.00239	0.00212
Finnish	0.00	0.00
European (Non-Finnish)	0.0000409	0.0000352
Middle Eastern	0.00239	0.00212
South Asian	0.00	0.00
Other	0.000165	0.000163

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.123
• ghis: 0.535

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.226

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Scarf2
• Phenotype: skeleton phenotype; immune system phenotype; limbs/digits/tail phenotype; hematopoietic system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
• Cellular component: focal adhesion;integral component of membrane
• Molecular function: protein binding