C12orf42

chromosome 12 open reading frame 42

Basic information

Region (hg38): 12:103237590-103495978

Links

ENSG00000179088 ∙ NCBI:374470 ∙ ∙ HGNC:24729 ∙ Uniprot:Q96LP6 ∙ 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 C12orf42 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf42 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	1		3
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	1	0

Variants in C12orf42

This is a list of pathogenic ClinVar variants found in the C12orf42 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-103306018-G-T		not specified	Uncertain significance (Aug 16, 2021)
12-103401648-T-G		not specified	Likely benign (Sep 17, 2021)
12-103401653-A-T		not specified	Uncertain significance (Aug 30, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf42	protein_coding	protein_coding	ENST00000378113	5	258381

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.75e-10	0.0229	124846	0	91	124937	0.000364

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.819	228	196	1.16	0.00000886	2335
Missense in Polyphen		62	51.329	1.2079		604
Synonymous	-1.77	95	75.5	1.26	0.00000346	729
Loss of Function	-0.841	13	10.1	1.29	4.24e-7	142

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000645	0.000644
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000526	0.0000463
European (Non-Finnish)	0.000482	0.000477
Middle Eastern	0.00	0.00
South Asian	0.000427	0.000425
Other	0.000331	0.000329

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.826
• rvis_EVS: 1.6
• rvis_percentile_EVS: 95.87

Haploinsufficiency Scores

• pHI: 0.0907
• hipred: N
• hipred_score: 0.153

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: 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: 1700113H08Rik