C15orf40

chromosome 15 open reading frame 40

Basic information

Region (hg38): 15:82988441-83011641

Links

ENSG00000169609 ∙ NCBI:123207 ∙ ∙ HGNC:28443 ∙ Uniprot:Q8WUR7 ∙ 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 C15orf40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C15orf40 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			2			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in C15orf40

This is a list of pathogenic ClinVar variants found in the C15orf40 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-82989090-G-T		not specified	Uncertain significance (Dec 26, 2023)
15-82989091-G-C		not specified	Uncertain significance (Aug 12, 2024)
15-82989125-C-T		not specified	Uncertain significance (Oct 29, 2024)
15-82989133-A-G		not specified	Uncertain significance (Oct 07, 2024)
15-82989142-G-A		not specified	Uncertain significance (Sep 03, 2024)
15-82989184-A-C		not specified	Uncertain significance (May 14, 2024)
15-82989185-A-G		not specified	Uncertain significance (May 06, 2024)
15-82989888-G-A		not specified	Uncertain significance (Jul 30, 2023)
15-82989921-T-G		not specified	Uncertain significance (May 24, 2024)
15-82989930-C-T		not specified	Uncertain significance (May 14, 2024)
15-82989943-G-A		not specified	Uncertain significance (Feb 06, 2023)
15-82989956-G-T		not specified	Uncertain significance (Nov 22, 2021)
15-82989977-C-A		not specified	Uncertain significance (Jul 12, 2022)
15-82990021-A-G		not specified	Uncertain significance (Aug 14, 2024)
15-82990029-T-C		not specified	Uncertain significance (Aug 30, 2022)
15-82990056-G-A		not specified	Uncertain significance (Oct 04, 2022)
15-83008492-T-C		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
15-83011534-C-T		not specified	Uncertain significance (Sep 09, 2021)
15-83011543-C-T		not specified	Uncertain significance (Oct 26, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C15orf40	protein_coding	protein_coding	ENST00000451195	5	23201

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.186	0.768	125586	0	162	125748	0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.625	106	89.4	1.19	0.00000428	1036
Missense in Polyphen		14	19.691	0.71097		262
Synonymous	-1.39	46	35.5	1.30	0.00000182	364
Loss of Function	1.66	2	6.58	0.304	2.76e-7	88

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)	0.0000724	0.0000703
Middle Eastern	0.00	0.00
South Asian	0.00332	0.00330
Other	0.000335	0.000326

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0807

Intolerance Scores

• loftool: 0.223
• rvis_EVS: 1.04
• rvis_percentile_EVS: 91.21

Haploinsufficiency Scores

• pHI: 0.0660
• hipred: N
• hipred_score: 0.123
• ghis: 0.423

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: 3110040N11Rik