C1orf198

chromosome 1 open reading frame 198

Basic information

Region (hg38): 1:230837119-230869589

Links

ENSG00000119280 ∙ NCBI:84886 ∙ ∙ HGNC:25900 ∙ Uniprot:Q9H425 ∙ 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 C1orf198 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf198 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	0

Variants in C1orf198

This is a list of pathogenic ClinVar variants found in the C1orf198 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-230843535-C-T		not specified	Uncertain significance (Oct 06, 2021)
1-230843669-C-A		not specified	Uncertain significance (Jul 28, 2021)
1-230868197-C-G		not specified	Uncertain significance (Oct 29, 2021)
1-230868218-C-T		not specified	Uncertain significance (Oct 05, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf198	protein_coding	protein_coding	ENST00000366663	4	32471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000629	0.915	125712	0	10	125722	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.799	162	193	0.838	0.0000108	2101
Missense in Polyphen		58	73.589	0.78816		831
Synonymous	1.41	69	85.6	0.806	0.00000532	652
Loss of Function	1.53	7	12.9	0.541	6.43e-7	135

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000154	0.000154
Ashkenazi Jewish	0.00	0.00
East Asian	0.000120	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000273	0.0000264
Middle Eastern	0.000120	0.000109
South Asian	0.0000327	0.0000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.854
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.236
• hipred: N
• hipred_score: 0.358
• ghis: 0.469

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: 2310022B05Rik
• Phenotype: behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); hematopoietic system phenotype; immune system phenotype

Gene ontology

• Cellular component: cytosol