PSORS1C1

psoriasis susceptibility 1 candidate 1

Basic information

Region (hg38): 6:31114750-31140092

Previous symbols: [ "C6orf16" ]

Links

ENSG00000204540 ∙ NCBI:170679 ∙ OMIM:613525 ∙ HGNC:17202 ∙ Uniprot:Q9UIG5 ∙ 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 PSORS1C1 gene.

• not_provided (75 variants)
• Inborn_genetic_diseases (48 variants)
• not_specified (32 variants)
• CDSN-related_disorder (17 variants)
• Peeling_skin_syndrome_1 (10 variants)
• Hypotrichosis_2 (5 variants)
• PSORS1C1-related_disorder (2 variants)
• Serum_phosphorus_normal_or_mildly_elevated (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PSORS1C1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000014068.3. 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						0
missense			14	2	3	19
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	14	2	3

Highest pathogenic variant AF is 0.0000423387

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PSORS1C1	protein_coding	protein_coding	ENST00000259881	4	25343

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000265	0.344	125318	0	46	125364	0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.681	62	79.0	0.784	0.00000382	972
Missense in Polyphen		5	3.7535	1.3321		49
Synonymous	0.861	26	32.2	0.807	0.00000179	320
Loss of Function	-0.249	5	4.43	1.13	1.89e-7	47

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00162	0.00162
European (Non-Finnish)	0.0000637	0.0000619
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000329	0.0000327
Other	0.000327	0.000327

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.856
• rvis_EVS: 1.88
• rvis_percentile_EVS: 97.25

Haploinsufficiency Scores

• pHI: 0.0987
• hipred: N
• hipred_score: 0.123
• ghis: 0.444

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0213

Gene Damage Prediction

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