C12orf76

chromosome 12 open reading frame 76

Basic information

Region (hg38): 12:110027027-110073636

Links

ENSG00000174456 ∙ NCBI:400073 ∙ ∙ HGNC:33790 ∙ Uniprot:Q8N812 ∙ 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 C12orf76 gene.

• Inborn genetic diseases (10 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf76 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						0
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			9	1		10
Total	0	0	9	1	0

Variants in C12orf76

This is a list of pathogenic ClinVar variants found in the C12orf76 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-110027746-C-T		not specified	Uncertain significance (Apr 25, 2023)
12-110027764-G-A		not specified	Uncertain significance (Apr 19, 2023)
12-110028533-A-G		not specified	Uncertain significance (May 04, 2022)
12-110028632-A-G		not specified	Uncertain significance (Jan 09, 2024)
12-110029633-T-C		not specified	Uncertain significance (May 11, 2022)
12-110030720-C-T		not specified	Uncertain significance (Jul 13, 2021)
12-110030725-T-C		not specified	Uncertain significance (Aug 28, 2023)
12-110033804-C-G		not specified	Likely benign (Apr 05, 2023)
12-110033847-G-A		not specified	Uncertain significance (Dec 22, 2023)
12-110033857-A-G		not specified	Uncertain significance (Sep 01, 2021)
12-110033884-A-G		not specified	Uncertain significance (Jun 03, 2022)
12-110036274-C-G		not specified	Uncertain significance (Feb 03, 2022)
12-110037407-C-G		not specified	Uncertain significance (Jun 14, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf76	protein_coding	protein_coding	ENST00000309050	4	45620

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
9.87e-7	0.103	125731	0	11	125742	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.438	63	73.6	0.856	0.00000378	892
Missense in Polyphen		4	5.826	0.68658		64
Synonymous	1.15	19	26.6	0.715	0.00000156	253
Loss of Function	-0.793	8	5.92	1.35	2.52e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000617	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.000326	0.000326
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.000326	0.000326
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.502
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.123
• ghis: 0.596

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Low	Medium
Primary Immunodeficiency	Medium	Low	Medium
Cancer	Medium	Medium	Medium