PSORS1C1

protein-coding

psoriasis susceptibility 1 candidate 1

Gene summary

This gene is one of several genes thought to confer susceptibility to psoriasis and systemic sclerosis, located on chromosome 6 near the major histocompatibility complex (MHC) class I region. [provided by RefSeq, Sep 2011]

Previous symbols:

C6orf16

MANE transcript

NM_014068.3

Inheritance

—

ClinVar variants

U:19B:6

Top phenotype

Inborn genetic diseases

gnomAD constraint

pLI —, LoF o/e 1.13

Max pathogenic AF

—

Genomic locus

chr6:31,114,750-31,140,092

External References & Databases

Ensembl (ENSG00000204540)

Transcript & Mutation Effects

hg38 • Region Span ~25.3 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to PSORS1C1 variants in ClinVar

8 Conditions Cataloged

not providedTotal: 82

Inborn genetic diseasesTotal: 52

not specifiedTotal: 50

CDSN-related disorderTotal: 21

Peeling skin syndrome 1Total: 10

Hypotrichosis 2Total: 5

PSORS1C1-related disorderTotal: 2

Serum phosphorus normal or mildly elevatedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_014068.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			18 clinvar	3 clinvar	3 clinvar	24
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	19	3	3	25

Highest pathogenic variant AF is 0.00004233874

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 6 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_014068.3	RefSeq	NP_054787.2	4	MANE Select
ENST00000259881.10	Ensembl	ENSP00000259881.9	4	MANE Select
ENST00000481450.2	Ensembl	ENSP00000447158.1	1	Standard
ENST00000481450.3	Ensembl	ENSP00000447158.1	1	Standard

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000259881
Coding exons: 4
Length: 25343
Individuals with no LoFs: 125318
Homozygous LoFs: 0
Heterozygous LoFs: 46
Defined: 125364
p: 0.000183

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.681	62	79.0	0.784	0.00000382	972
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000054	0.000054	rare
Finnish	0.0016	0.0016	notable
European (Non-Finnish)	0.000064	0.000062	rare
South Asian	0.000033	0.000033	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Intolerance Scores

LoFtool: 0.856
RVIS EVS: 1.88
RVIS percentile EVS: 97.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0213

Gene Damage Prediction

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