C12orf40

chromosome 12 open reading frame 40

Basic information

Region (hg38): 12:39626166-39908300

Links

ENSG00000180116 ∙ NCBI:283461 ∙ ∙ HGNC:26846 ∙ Uniprot:Q86WS4 ∙ 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 C12orf40 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf40 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			4			4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding			9			9
Total	0	0	13	0	0

Variants in C12orf40

This is a list of pathogenic ClinVar variants found in the C12orf40 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-39646358-A-ATT		Spermatogenic Failure	Pathogenic (-)
12-39647842-A-G		not specified	Uncertain significance (Oct 14, 2021)
12-39650239-C-T		not specified	Uncertain significance (Oct 29, 2021)
12-39682706-C-G		not specified	Uncertain significance (Aug 09, 2021)
12-39683063-A-C		not specified	Uncertain significance (Oct 26, 2021)
12-39760097-A-G		not specified	Uncertain significance (Dec 11, 2023)
12-39760234-G-A		not specified	Uncertain significance (Sep 27, 2022)
12-39764499-G-C		not specified	Uncertain significance (Dec 16, 2023)
12-39764544-C-A		not specified	Uncertain significance (Jan 23, 2024)
12-39764567-A-C		not specified	Uncertain significance (Jan 04, 2022)
12-39764815-C-T		not specified	Uncertain significance (Jun 21, 2021)
12-39830124-G-A		not specified	Uncertain significance (Feb 27, 2024)
12-39830176-T-C		not specified	Uncertain significance (Mar 04, 2024)
12-39864777-G-A		not specified	Uncertain significance (Jan 09, 2024)
12-39864819-C-T		not specified	Uncertain significance (Nov 15, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf40	protein_coding	protein_coding	ENST00000324616	13	282134

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.29e-13	0.0888	124701	0	28	124729	0.000112

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.368	337	319	1.06	0.0000148	4371
Missense in Polyphen		57	60.841	0.93687		914
Synonymous	0.0930	108	109	0.989	0.00000541	1098
Loss of Function	0.672	22	25.7	0.857	0.00000117	370

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000314	0.0000314
Ashkenazi Jewish	0.000499	0.000497
East Asian	0.000508	0.000501
Finnish	0.0000490	0.0000464
European (Non-Finnish)	0.0000837	0.0000795
Middle Eastern	0.000508	0.000501
South Asian	0.0000723	0.0000654
Other	0.000176	0.000165

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.898
• rvis_EVS: 1.07
• rvis_percentile_EVS: 91.61

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123

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: CN725425

Gene ontology

• Molecular function: protein binding