SORCS1

sortilin related VPS10 domain containing receptor 1

Basic information

Region (hg38): 10:106573663-107164706

Links

ENSG00000108018 ∙ NCBI:114815 ∙ OMIM:606283 ∙ HGNC:16697 ∙ Uniprot:Q8WY21 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the SORCS1 gene.

• not_specified (142 variants)
• not_provided (11 variants)
• Prostate_cancer (1 variants)
• Alzheimer_disease_6 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the SORCS1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000052918.5. 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				5	4	9
missense			134	3	2	139
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	134	8	6

Highest pathogenic variant AF is 6.840694e-7

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
SORCS1	protein_coding	protein_coding	ENST00000344440	27	590872

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.559	0.441	125704	0	44	125748	0.000175

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.30	566	660	0.857	0.0000355	7771
Missense in Polyphen		142	218.52	0.64984		2643
Synonymous	0.625	250	263	0.951	0.0000152	2353
Loss of Function	5.98	15	68.3	0.220	0.00000370	757

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000619	0.000619
Ashkenazi Jewish	0.000199	0.000198
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000141	0.000141
Middle Eastern	0.0000544	0.0000544
South Asian	0.000229	0.000229
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Ectoderm Differentiation (Consensus)

Recessive Scores

• pRec: 0.136

Intolerance Scores

• loftool: 0.644
• rvis_EVS: -1.14
• rvis_percentile_EVS: 6.36

Haploinsufficiency Scores

• pHI: 0.324
• hipred: Y
• hipred_score: 0.693
• ghis: 0.552

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.255

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Sorcs1
• Phenotype: homeostasis/metabolism 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)

Gene ontology

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