PSORS1C2

psoriasis susceptibility 1 candidate 2

Basic information

Region (hg38): 6:31137533-31139066

Previous symbols: [ "C6orf17" ]

Links

ENSG00000204538 ∙ NCBI:170680 ∙ OMIM:613526 ∙ HGNC:17199 ∙ Uniprot:Q9UIG4 ∙ 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 PSORS1C2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSORS1C2 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						0
missense			6		1	7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1	1	6	8
Total	0	0	7	1	7

Variants in PSORS1C2

This is a list of pathogenic ClinVar variants found in the PSORS1C2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31137986-G-A		not specified	Uncertain significance (Feb 14, 2023)
6-31138022-G-A		not specified	Uncertain significance (Sep 21, 2023)
6-31138141-C-T		not specified	Uncertain significance (Aug 14, 2023)
6-31138153-C-G		not specified	Uncertain significance (Jun 16, 2023)
6-31138156-G-A		not specified	Uncertain significance (Mar 19, 2024)
6-31138196-C-T		not specified	Uncertain significance (Oct 25, 2022)
6-31138211-C-T			Benign (Jun 15, 2018)
6-31138237-G-A		not specified	Uncertain significance (Mar 06, 2023)
6-31138646-T-C			Benign (Aug 02, 2017)
6-31138682-C-A		PSORS1C1-related disorder	Benign (Nov 06, 2019)
6-31138712-G-A		PSORS1C1-related disorder	Benign (Oct 21, 2019)
6-31138721-C-T		not specified	Uncertain significance (Dec 18, 2023)
6-31138722-G-A		PSORS1C1-related disorder	Benign (Nov 08, 2019)
6-31138739-C-T		PSORS1C1-related disorder	Benign (Dec 09, 2019)
6-31138746-G-A		PSORS1C1-related disorder	Benign (Feb 25, 2020)
6-31138746-G-T		not specified	Likely benign (Jul 19, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSORS1C2	protein_coding	protein_coding	ENST00000259845	2	1815

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00249	0.564	110469	766	14493	125728	0.0626

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.260	65	71.2	0.913	0.00000376	834
Missense in Polyphen		26	30.38	0.85582		353
Synonymous	0.933	22	28.3	0.777	0.00000162	290
Loss of Function	0.296	4	4.69	0.853	2.71e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0747	0.0695
Ashkenazi Jewish	0.0450	0.0297
East Asian	0.0128	0.0117
Finnish	0.105	0.0950
European (Non-Finnish)	0.102	0.0855
Middle Eastern	0.0128	0.0117
South Asian	0.0700	0.0545
Other	0.0781	0.0619

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.779
• rvis_EVS: 1.32
• rvis_percentile_EVS: 94.09

Haploinsufficiency Scores

• pHI: 0.113
• hipred: N
• hipred_score: 0.123
• ghis: 0.405

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0000591

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Psors1c2

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;extracellular region
• Molecular function: molecular_function