SORCS2

sortilin related VPS10 domain containing receptor 2, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 4:7192537-7742836

Links

ENSG00000184985 ∙ NCBI:57537 ∙ OMIM:606284 ∙ HGNC:16698 ∙ Uniprot:Q96PQ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SORCS2 gene.

• Inborn genetic diseases (113 variants)
• not provided (18 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SORCS2 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				2	9	11
missense			68	4	1	73
nonsense						0
start loss						0
frameshift						0
inframe indel			1			1
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			38	5	1	44
Total	0	0	107	11	11

Variants in SORCS2

This is a list of pathogenic ClinVar variants found in the SORCS2 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-7192654-A-C		not specified	Uncertain significance (Apr 07, 2022)
4-7192681-G-T		not specified	Uncertain significance (May 06, 2022)
4-7192683-C-T		not specified	Uncertain significance (Oct 06, 2021)
4-7192690-C-T		not specified	Uncertain significance (Apr 18, 2023)
4-7192692-A-C		not specified	Uncertain significance (Nov 09, 2021)
4-7192693-C-G		not specified	Uncertain significance (Jun 09, 2022)
4-7192699-G-A		not specified	Uncertain significance (Mar 07, 2024)
4-7192702-C-A		not specified	Uncertain significance (Sep 15, 2021)
4-7192705-C-G			Uncertain significance (Sep 01, 2023)
4-7192716-G-A		not specified	Uncertain significance (Nov 28, 2023)
4-7192725-C-T		not specified	Uncertain significance (Apr 07, 2022)
4-7192725-C-CCGCCGCGCT			Uncertain significance (Sep 01, 2023)
4-7192731-C-T		not specified	Uncertain significance (Oct 17, 2023)
4-7192744-C-T		not specified	Uncertain significance (Sep 06, 2022)
4-7192777-G-C		not specified	Uncertain significance (Apr 07, 2023)
4-7192804-C-T		not specified	Uncertain significance (Apr 07, 2023)
4-7192834-A-C		not specified	Uncertain significance (Feb 22, 2023)
4-7192866-G-A		not specified	Uncertain significance (Aug 08, 2022)
4-7192881-G-A		not specified	Uncertain significance (Aug 20, 2023)
4-7193083-C-G		not specified	Uncertain significance (Apr 07, 2022)
4-7193110-C-T		not specified	Uncertain significance (Dec 21, 2023)
4-7396304-C-T		not specified	Uncertain significance (Sep 06, 2022)
4-7396317-C-G		not specified	Uncertain significance (May 11, 2022)
4-7433330-G-A		not specified	Uncertain significance (Oct 03, 2022)
4-7433352-A-T		not specified	Uncertain significance (Jun 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SORCS2	protein_coding	protein_coding	ENST00000507866	27	550290

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00317	0.997	124617	0	24	124641	0.0000963

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.585	589	630	0.934	0.0000412	7349
Missense in Polyphen		169	215.27	0.78506		2269
Synonymous	-2.56	347	291	1.19	0.0000221	2356
Loss of Function	5.01	16	56.7	0.282	0.00000267	648

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000437	0.000436
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.000119	0.000115
Middle Eastern	0.00	0.00
South Asian	0.0000388	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0996

Intolerance Scores

• loftool: 0.693
• rvis_EVS: -0.41
• rvis_percentile_EVS: 25.87

Haploinsufficiency Scores

• pHI: 0.551
• hipred: N
• hipred_score: 0.492
• ghis: 0.503

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.384

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sorcs2
• Phenotype: homeostasis/metabolism phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: neuropeptide signaling pathway
• Cellular component: membrane;integral component of membrane
• Molecular function: neuropeptide receptor activity