SORCS1

sortilin related VPS10 domain containing receptor 1

Basic information

Region (hg38): 10:106573662-107164706

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.

• Inborn genetic diseases (43 variants)
• not provided (11 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.

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			43	1	2	46
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding		1				1
Total	0	1	43	4	6

Variants in SORCS1

This is a list of pathogenic ClinVar variants found in the SORCS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-106579202-G-A		Alzheimer disease 6	Likely pathogenic (May 12, 2022)
10-106579243-G-A		Malignant tumor of prostate	Uncertain significance (-)
10-106579376-A-G		not specified	Uncertain significance (Feb 06, 2023)
10-106579388-C-T			Likely benign (Mar 01, 2023)
10-106597428-G-A		not specified	Uncertain significance (Nov 13, 2023)
10-106597431-T-C		not specified	Uncertain significance (Feb 28, 2024)
10-106607170-T-G		not specified	Uncertain significance (Dec 07, 2023)
10-106607212-T-C		not specified	Uncertain significance (Sep 17, 2021)
10-106607221-A-G		not specified	Uncertain significance (Apr 21, 2022)
10-106607264-C-T		not specified	Uncertain significance (Oct 04, 2022)
10-106618233-T-C		not specified	Uncertain significance (Oct 26, 2021)
10-106618246-T-C		not specified	Uncertain significance (Feb 27, 2024)
10-106620490-C-T		not specified	Uncertain significance (Jul 19, 2023)
10-106629221-G-A			Likely benign (May 25, 2018)
10-106629267-C-T		not specified	Uncertain significance (Mar 28, 2022)
10-106629292-C-T		not specified	Uncertain significance (Oct 03, 2022)
10-106629338-C-T		not specified	Likely benign (Oct 05, 2023)
10-106629375-C-T		not specified	Uncertain significance (Aug 02, 2023)
10-106652402-G-C		not specified	Uncertain significance (Aug 08, 2022)
10-106652413-T-C		not specified	Uncertain significance (Sep 13, 2023)
10-106652460-C-T			Benign (Jul 23, 2018)
10-106652465-G-A		not specified	Uncertain significance (Jan 23, 2024)
10-106652491-G-T			Benign (Jun 14, 2018)
10-106652516-C-T		not specified	Uncertain significance (May 24, 2023)
10-106652552-A-G		not specified	Uncertain significance (Jul 13, 2021)

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