C6orf15

chromosome 6 open reading frame 15

Basic information

Region (hg38): 6:31111222-31112575

Links

ENSG00000204542 ∙ NCBI:29113 ∙ OMIM:611401 ∙ HGNC:13927 ∙ Uniprot:Q6UXA7 ∙ 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 C6orf15 gene.

• Inborn genetic diseases (6 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C6orf15 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				1		1
missense			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	1	0

Variants in C6orf15

This is a list of pathogenic ClinVar variants found in the C6orf15 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-31111530-G-A		not specified	Uncertain significance (Jul 26, 2021)
6-31111573-T-C			Likely benign (Dec 01, 2022)
6-31111695-C-T		not specified	Uncertain significance (Aug 04, 2021)
6-31112057-G-A		not specified	Uncertain significance (Nov 16, 2021)
6-31112118-C-T		not specified	Uncertain significance (Aug 12, 2021)
6-31112205-A-G		not specified	Uncertain significance (Aug 12, 2021)
6-31112207-G-A		not specified	Uncertain significance (Sep 15, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C6orf15	protein_coding	protein_coding	ENST00000259870	2	1337

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0105	0.843	125702	0	20	125722	0.0000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.12	150	194	0.774	0.0000108	2047
Missense in Polyphen		46	58.954	0.78026		607
Synonymous	0.881	66	75.7	0.871	0.00000434	724
Loss of Function	1.18	4	7.47	0.536	4.22e-7	64

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000184	0.000178
Ashkenazi Jewish	0.000101	0.0000993
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000817	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.000363	0.000163
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.829
• rvis_EVS: 1.75
• rvis_percentile_EVS: 96.69

Haploinsufficiency Scores

• pHI: 0.0703
• hipred: N
• hipred_score: 0.123
• ghis: 0.469

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: 2300002M23Rik
• Phenotype: growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan)

Gene ontology

• Biological process: biological_process
• Cellular component: cellular_component;extracellular region
• Molecular function: molecular_function