C1orf74

chromosome 1 open reading frame 74

Basic information

Region (hg38): 1:209779208-209784559

Links

ENSG00000162757 ∙ NCBI:148304 ∙ ∙ HGNC:26319 ∙ Uniprot:Q96LT6 ∙ 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 C1orf74 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf74 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			7			7
Total	0	0	9	0	0

Variants in C1orf74

This is a list of pathogenic ClinVar variants found in the C1orf74 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-209780484-G-A		not specified	Uncertain significance (Nov 17, 2022)
1-209780527-G-A		not specified	Uncertain significance (Feb 23, 2023)
1-209780592-G-A		not specified	Uncertain significance (Dec 07, 2023)
1-209781373-A-G		not specified	Uncertain significance (May 25, 2022)
1-209781384-G-A		not specified	Uncertain significance (Nov 27, 2024)
1-209781402-C-T		not specified	Uncertain significance (Nov 07, 2024)
1-209781403-G-A		not specified	Uncertain significance (Oct 30, 2023)
1-209781421-G-A		not specified	Uncertain significance (Sep 27, 2022)
1-209782089-G-A		not specified	Uncertain significance (Oct 03, 2023)
1-209782092-G-A		not specified	Likely benign (Aug 19, 2024)
1-209782902-G-C		not specified	Uncertain significance (Nov 09, 2021)
1-209783054-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf74	protein_coding	protein_coding	ENST00000294811	1	2244

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0153	0.888	125734	0	14	125748	0.0000557

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.736	117	142	0.826	0.00000726	1718
Missense in Polyphen		30	37.349	0.80322		505
Synonymous	1.22	48	60.0	0.799	0.00000285	600
Loss of Function	1.39	4	8.33	0.480	5.40e-7	89

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000210	0.000210
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000440	0.0000439
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.525
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.49

Haploinsufficiency Scores

• pHI: 0.126
• hipred: N
• hipred_score: 0.169
• ghis: 0.522

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• 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: A130010J15Rik