C1orf87

chromosome 1 open reading frame 87

Basic information

Region (hg38): 1:59987269-60073770

Links

ENSG00000162598 ∙ NCBI:127795 ∙ OMIM:618860 ∙ HGNC:28547 ∙ Uniprot:Q8N0U7 ∙ 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 C1orf87 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C1orf87 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					1	1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	4	0	1

Variants in C1orf87

This is a list of pathogenic ClinVar variants found in the C1orf87 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-59990819-C-A			Benign (Aug 14, 2017)
1-59990830-A-G		not specified	Uncertain significance (Jul 20, 2021)
1-59997671-G-A		not specified	Uncertain significance (Sep 16, 2021)
1-60039918-A-G		not specified	Uncertain significance (Jul 20, 2021)
1-60040033-C-T		not specified	Uncertain significance (Aug 02, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C1orf87	protein_coding	protein_coding	ENST00000371201	11	86502

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.18e-25	0.0000267	125441	1	305	125747	0.00122

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.215	293	283	1.04	0.0000141	3595
Missense in Polyphen		48	54.924	0.87394		796
Synonymous	-0.747	113	103	1.09	0.00000498	1019
Loss of Function	-1.24	33	26.2	1.26	0.00000127	329

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0145	0.0146
Ashkenazi Jewish	0.0000998	0.0000992
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.000250	0.000246
Middle Eastern	0.000109	0.000109
South Asian	0.000562	0.000523
Other	0.000979	0.000978

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.969
• rvis_EVS: 1.73
• rvis_percentile_EVS: 96.6

Haploinsufficiency Scores

• pHI: 0.0580
• hipred: N
• hipred_score: 0.123

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: Gm12695