C1orf174

chromosome 1 open reading frame 174

Basic information

Region (hg38): 1:3889125-3900293

Links

ENSG00000198912 ∙ NCBI:339448 ∙ ∙ HGNC:27915 ∙ Uniprot:Q8IYL3 ∙ 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 C1orf174 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf174 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 C1orf174

This is a list of pathogenic ClinVar variants found in the C1orf174 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-3890748-C-T		not specified	Uncertain significance (Jul 09, 2021)
1-3890975-A-G		not specified	Uncertain significance (Oct 27, 2021)
1-3892968-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-3900177-G-A		not specified	Uncertain significance (Jul 20, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf174	protein_coding	protein_coding	ENST00000361605	4	11169

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000107	0.606	125706	0	42	125748	0.000167

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0232	144	145	0.995	0.00000839	1584
Missense in Polyphen		47	49.609	0.94741		536
Synonymous	-0.149	60	58.6	1.02	0.00000398	482
Loss of Function	0.700	7	9.31	0.752	5.76e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000492	0.000492
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000108	0.000105
Middle Eastern	0.000598	0.000598
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0923

Intolerance Scores

• loftool: 0.876
• rvis_EVS: 1.06
• rvis_percentile_EVS: 91.58

Haploinsufficiency Scores

• pHI: 0.166
• hipred: N
• hipred_score: 0.146
• ghis: 0.507

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: A430005L14Rik
• Phenotype: homeostasis/metabolism phenotype

Gene ontology

• Cellular component: nucleus
• Molecular function: protein binding