C15orf48

chromosome 15 open reading frame 48, the group of MicroRNA protein coding host genes

Basic information

Region (hg38): 15:45430579-45448761

Links

ENSG00000166920 ∙ NCBI:84419 ∙ OMIM:608409 ∙ HGNC:29898 ∙ Uniprot:Q9C002 ∙ 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 C15orf48 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C15orf48 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			1			1
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	1	0	0

Variants in C15orf48

This is a list of pathogenic ClinVar variants found in the C15orf48 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-45431028-G-C		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C15orf48	protein_coding	protein_coding	ENST00000344300	4	18233

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000555	0.275	124828	1	915	125744	0.00365

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.397	37	44.4	0.833	0.00000226	541
Missense in Polyphen		9	14.485	0.62132		189
Synonymous	1.17	10	15.9	0.628	0.00000102	145
Loss of Function	-0.298	6	5.26	1.14	2.87e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00701	0.00690
Ashkenazi Jewish	0.000502	0.000496
East Asian	0.00225	0.00223
Finnish	0.00134	0.00134
European (Non-Finnish)	0.00566	0.00561
Middle Eastern	0.00225	0.00223
South Asian	0.00141	0.00137
Other	0.00316	0.00310

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.778
• rvis_EVS: 0.08
• rvis_percentile_EVS: 59.43

Haploinsufficiency Scores

• pHI: 0.0693
• hipred: N
• hipred_score: 0.144
• ghis: 0.495

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: AA467197