OSCP1

organic solute carrier partner 1, the group of Small nucleolar RNA protein coding host genes

Basic information

Region (hg38): 1:36415827-36450451

Previous symbols: [ "C1orf102" ]

Links

ENSG00000116885 ∙ NCBI:127700 ∙ OMIM:608854 ∙ HGNC:29971 ∙ Uniprot:Q8WVF1 ∙ 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 OSCP1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OSCP1 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			26	1		27
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1		1
Total	0	0	26	2	0

Variants in OSCP1

This is a list of pathogenic ClinVar variants found in the OSCP1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-36418171-C-T		not specified	Uncertain significance (Feb 12, 2025)
1-36418225-T-C		not specified	Uncertain significance (Feb 08, 2025)
1-36418240-C-T		not specified	Uncertain significance (Aug 10, 2024)
1-36418245-C-T		not specified	Uncertain significance (Jan 27, 2025)
1-36419004-A-G		not specified	Uncertain significance (Jul 05, 2023)
1-36419015-T-A		not specified	Uncertain significance (Nov 25, 2024)
1-36419046-G-A		not specified	Uncertain significance (Jun 26, 2024)
1-36420491-G-A		not specified	Uncertain significance (Dec 09, 2023)
1-36420509-C-T		not specified	Uncertain significance (Dec 10, 2024)
1-36420510-G-A		not specified	Uncertain significance (Feb 25, 2025)
1-36420530-C-A		not specified	Uncertain significance (Oct 01, 2024)
1-36420615-C-G		not specified	Uncertain significance (Nov 17, 2023)
1-36422213-G-C		not specified	Uncertain significance (May 10, 2022)
1-36422780-A-C		not specified	Uncertain significance (Feb 13, 2024)
1-36422792-C-T		not specified	Uncertain significance (May 31, 2023)
1-36422829-C-T		not specified	Uncertain significance (Sep 11, 2024)
1-36423369-A-T		not specified	Uncertain significance (Dec 13, 2022)
1-36423433-T-C		not specified	Uncertain significance (Oct 06, 2024)
1-36423438-T-C		not specified	Uncertain significance (Dec 07, 2021)
1-36423439-G-C		not specified	Uncertain significance (Jan 17, 2025)
1-36423459-A-G		not specified	Uncertain significance (Nov 30, 2022)
1-36428329-C-T			Likely benign (Mar 01, 2023)
1-36431828-T-A		not specified	Uncertain significance (Aug 08, 2023)
1-36432436-G-A		not specified	Uncertain significance (Nov 16, 2022)
1-36432455-C-A		not specified	Likely benign (Oct 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OSCP1	protein_coding	protein_coding	ENST00000235532	10	34659

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
7.03e-10	0.437	125698	0	50	125748	0.000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	172	219	0.787	0.0000117	2481
Missense in Polyphen		52	65.15	0.79816		737
Synonymous	0.347	82	86.1	0.952	0.00000466	736
Loss of Function	1.05	17	22.4	0.760	0.00000137	241

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000270	0.000268
Ashkenazi Jewish	0.00	0.00
East Asian	0.000653	0.000653
Finnish	0.00	0.00
European (Non-Finnish)	0.000159	0.000158
Middle Eastern	0.000653	0.000653
South Asian	0.000436	0.000425
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in drug clearance in the placenta. {ECO:0000269|PubMed:16006562}.

Recessive Scores

• pRec: 0.0985

Intolerance Scores

• loftool: 0.924
• rvis_EVS: 0.58
• rvis_percentile_EVS: 82.17

Haploinsufficiency Scores

• pHI: 0.164
• hipred: N
• hipred_score: 0.204
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.231

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oscp1

Gene ontology

• Cellular component: basal plasma membrane