C1orf116

chromosome 1 open reading frame 116

Basic information

Region (hg38): 1:207018522-207032756

Links

ENSG00000182795 ∙ NCBI:79098 ∙ OMIM:611680 ∙ HGNC:28667 ∙ Uniprot:Q9BW04 ∙ 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 C1orf116 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf116 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			7	1		8
nonsense						0
start loss						0
frameshift				1		1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	2	0

Variants in C1orf116

This is a list of pathogenic ClinVar variants found in the C1orf116 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-207022046-G-C		not specified	Uncertain significance (Oct 06, 2021)
1-207022185-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-207022539-C-A		not specified	Uncertain significance (Aug 17, 2021)
1-207022727-G-C		not specified	Uncertain significance (Aug 02, 2021)
1-207022980-G-A		not specified	Uncertain significance (Sep 27, 2021)
1-207023150-C-T		not specified	Likely benign (Sep 16, 2021)
1-207024907-A-T		not specified	Uncertain significance (Sep 01, 2021)
1-207027530-G-GT			Likely benign (Apr 01, 2023)
1-207027584-C-G		not specified	Uncertain significance (Sep 27, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf116	protein_coding	protein_coding	ENST00000359470	3	14236

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00171	0.993	125687	0	61	125748	0.000243

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.386	361	341	1.06	0.0000187	3817
Missense in Polyphen		101	101.22	0.99787		1190
Synonymous	1.15	121	138	0.875	0.00000740	1318
Loss of Function	2.46	8	19.8	0.404	0.00000120	208

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000858	0.000671
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000291	0.000281
Middle Eastern	0.000219	0.000217
South Asian	0.000348	0.000327
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative androgen-specific receptor. {ECO:0000269|PubMed:15525603}.

Recessive Scores

• pRec: 0.0931

Intolerance Scores

• loftool: 0.833
• rvis_EVS: 2.8
• rvis_percentile_EVS: 99.05

Haploinsufficiency Scores

• pHI: 0.0452
• hipred: N
• hipred_score: 0.316

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: AA986860