SORCS3

sortilin related VPS10 domain containing receptor 3

Basic information

Region (hg38): 10:104641290-105265242

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.

• not_specified (162 variants)
• not_provided (13 variants)
• SORCS3-related_disorder (4 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. These statistics are base on transcript: NM_000014978.3. Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				4	4	8
missense			160	6	4	170
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	160	10	8

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