C5orf15

chromosome 5 open reading frame 15

Basic information

Region (hg38): 5:133955509-133968674

Links

ENSG00000113583 ∙ NCBI:56951 ∙ ∙ HGNC:20656 ∙ Uniprot:Q8NC54 ∙ 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 C5orf15 gene.

• Inborn genetic diseases (5 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C5orf15 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			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	0	0

Variants in C5orf15

This is a list of pathogenic ClinVar variants found in the C5orf15 region.

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

Position	Type	Phenotype	Significance	ClinVar
5-133959676-C-T		not specified	Uncertain significance (Jun 18, 2021)
5-133959793-T-C		not specified	Uncertain significance (Jul 13, 2021)
5-133959804-T-C		not specified	Uncertain significance (Jul 09, 2021)
5-133959999-G-A		not specified	Uncertain significance (Jul 16, 2021)
5-133968535-A-C		not specified	Uncertain significance (Nov 09, 2021)
5-133968553-C-A		not specified	Uncertain significance (Aug 10, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C5orf15	protein_coding	protein_coding	ENST00000231512	3	13278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0503	0.868	125703	0	43	125746	0.000171

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.392	134	147	0.909	0.00000766	1735
Missense in Polyphen		27	40.067	0.67388		545
Synonymous	-0.140	62	60.6	1.02	0.00000353	540
Loss of Function	1.44	3	7.16	0.419	3.02e-7	98

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00147	0.00147
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000716	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.0000329	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0843

Intolerance Scores

• loftool: 0.215
• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.263
• hipred: N
• hipred_score: 0.123
• ghis: 0.549

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: 9530068E07Rik