C15orf39

chromosome 15 open reading frame 39

Basic information

Region (hg38): 15:75195643-75212169

Links

ENSG00000167173 ∙ NCBI:56905 ∙ ∙ HGNC:24497 ∙ Uniprot:Q6ZRI6 ∙ 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 C15orf39 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C15orf39 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			17	2		19
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	17	2	0

Variants in C15orf39

This is a list of pathogenic ClinVar variants found in the C15orf39 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-75206088-A-G		not specified	Uncertain significance (Jul 16, 2024)
15-75206214-C-T		not specified	Uncertain significance (Jul 13, 2021)
15-75206596-G-T		not specified	Uncertain significance (Oct 05, 2021)
15-75206602-C-G		not specified	Likely benign (Oct 22, 2021)
15-75206629-T-C		not specified	Uncertain significance (Sep 17, 2021)
15-75206866-A-G		not specified	Uncertain significance (Nov 08, 2021)
15-75206953-T-A		not specified	Uncertain significance (Jan 24, 2024)
15-75206974-G-A		not specified	Uncertain significance (Oct 26, 2021)
15-75207049-A-G		not specified	Uncertain significance (Nov 12, 2021)
15-75207166-C-T		not specified	Uncertain significance (Aug 09, 2021)
15-75207301-A-G		not specified	Uncertain significance (Nov 09, 2021)
15-75207427-C-T		not specified	Uncertain significance (Sep 01, 2021)
15-75207435-G-A		not specified	Uncertain significance (Oct 22, 2021)
15-75207586-G-A		not specified	Uncertain significance (Jan 23, 2024)
15-75207711-C-G		not specified	Uncertain significance (Sep 17, 2021)
15-75207823-G-A			Likely benign (Mar 01, 2023)
15-75207850-C-A		not specified	Uncertain significance (Jul 16, 2021)
15-75208054-C-T		not specified	Uncertain significance (Aug 13, 2021)
15-75208281-C-T		not specified	Uncertain significance (Aug 12, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C15orf39	protein_coding	protein_coding	ENST00000360639	2	16527

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00541	0.994	125718	0	29	125747	0.000115

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	533	611	0.873	0.0000352	6538
Missense in Polyphen		67	100.51	0.66661		1034
Synonymous	0.719	249	264	0.944	0.0000152	2431
Loss of Function	3.24	9	27.3	0.330	0.00000156	294

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000159	0.000150
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000567	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.000184	0.000176
Middle Eastern	0.0000567	0.0000544
South Asian	0.000134	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0907

Intolerance Scores

• rvis_EVS: 0.72
• rvis_percentile_EVS: 85.88

Haploinsufficiency Scores

• pHI: 0.138
• hipred: N
• hipred_score: 0.379
• ghis: 0.469

Essentials

• essential_gene_CRISPR: E
• 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: 1700017B05Rik

Gene ontology

• Cellular component: cytosol