SORCS3

sortilin related VPS10 domain containing receptor 3

Basic information

Region (hg38): 10:104641289-105265242

Links

ENSG00000156395 ∙ NCBI:22986 ∙ OMIM:606285 ∙ HGNC:16699 ∙ Uniprot:Q9UPU3 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SORCS3 gene.

• Inborn genetic diseases (45 variants)
• not provided (12 variants)
• SORCS3-related condition (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SORCS3 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				3	4	7
missense			45	1	4	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	45	4	9

Variants in SORCS3

This is a list of pathogenic ClinVar variants found in the SORCS3 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-104641362-G-A			Benign (Dec 31, 2019)
10-104641386-C-G		not specified	Uncertain significance (Mar 11, 2024)
10-104641421-G-A			Benign (Apr 05, 2018)
10-104641442-G-A		not specified	Uncertain significance (Jun 09, 2022)
10-104641461-G-A		not specified	Uncertain significance (May 25, 2022)
10-104641464-C-T		not specified	Uncertain significance (Jan 31, 2022)
10-104641479-C-T		not specified	Uncertain significance (Dec 16, 2022)
10-104641565-G-C		not specified	Uncertain significance (Aug 09, 2021)
10-104641577-C-A		SORCS3-related disorder	Likely benign (Apr 08, 2023)
10-104641591-G-T		not specified	Uncertain significance (Dec 16, 2022)
10-104641633-G-C		not specified	Uncertain significance (Feb 10, 2022)
10-104641647-G-T		not specified	Uncertain significance (Nov 15, 2021)
10-104641649-A-T		not specified	Uncertain significance (Nov 15, 2021)
10-104641832-A-C		not specified	Uncertain significance (Nov 22, 2023)
10-104641850-G-A		not specified	Uncertain significance (Dec 07, 2022)
10-104641882-C-A		not specified	Uncertain significance (Feb 14, 2023)
10-104641908-C-T		not specified	Uncertain significance (Jun 07, 2023)
10-104641916-A-T		not specified	Uncertain significance (Nov 20, 2023)
10-104641922-G-T		not specified	Uncertain significance (Jul 20, 2022)
10-104915823-T-G			Benign (Dec 20, 2018)
10-104915876-G-A		not specified	Uncertain significance (Mar 17, 2023)
10-104977347-A-T		not specified	Uncertain significance (Jan 09, 2024)
10-104977413-C-T		not specified	Uncertain significance (Feb 22, 2023)
10-104977416-C-T		not specified	Uncertain significance (Jul 14, 2021)
10-104977484-G-C		not specified	Uncertain significance (Jul 11, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SORCS3	protein_coding	protein_coding	ENST00000369701	27	624135

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000374	1.00	125713	0	35	125748	0.000139

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.52	542	651	0.832	0.0000345	7925
Missense in Polyphen		119	191.75	0.62061		2386
Synonymous	-0.147	263	260	1.01	0.0000148	2423
Loss of Function	4.98	20	62.5	0.320	0.00000300	741

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000334	0.000333
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000168	0.000167
Middle Eastern	0.000109	0.000109
South Asian	0.000101	0.0000980
Other	0.000327	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.108

Intolerance Scores

• loftool: 0.531
• rvis_EVS: -1.17
• rvis_percentile_EVS: 6.04

Haploinsufficiency Scores

• pHI: 0.815
• hipred: Y
• hipred_score: 0.711
• ghis: 0.581

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.276

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sorcs3
• Phenotype: 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan)

Gene ontology

• Biological process: neuropeptide signaling pathway;learning;memory;regulation of long-term synaptic depression
• Cellular component: membrane;glutamatergic synapse;integral component of postsynaptic density membrane
• Molecular function: neuropeptide receptor activity