C12orf60

chromosome 12 open reading frame 60

Basic information

Region (hg38): 12:14803666-14906586

Links

ENSG00000182993 ∙ NCBI:144608 ∙ ∙ HGNC:28726 ∙ Uniprot:Q5U649 ∙ 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 C12orf60 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf60 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		2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			19			19
Total	0	0	20	1	0

Variants in C12orf60

This is a list of pathogenic ClinVar variants found in the C12orf60 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-14806023-C-G		not specified	Uncertain significance (Jan 05, 2022)
12-14806026-T-C		not specified	Uncertain significance (Dec 27, 2023)
12-14806073-T-C		not specified	Uncertain significance (Oct 10, 2023)
12-14806073-T-G		not specified	Uncertain significance (May 26, 2024)
12-14806090-C-A		not specified	Uncertain significance (Apr 14, 2022)
12-14806118-A-G		not specified	Uncertain significance (Dec 20, 2023)
12-14806148-G-A		not specified	Uncertain significance (Feb 12, 2024)
12-14806152-G-A		not specified	Uncertain significance (Jun 06, 2023)
12-14806176-C-G		not specified	Uncertain significance (Dec 16, 2022)
12-14806259-G-T		not specified	Uncertain significance (Oct 04, 2022)
12-14806298-G-C		not specified	Uncertain significance (Oct 14, 2021)
12-14806311-C-T		not specified	Uncertain significance (Dec 14, 2023)
12-14806330-A-C		not specified	Uncertain significance (Apr 27, 2022)
12-14806346-A-T		not specified	Uncertain significance (Jun 18, 2021)
12-14806438-C-G		not specified	Uncertain significance (Mar 20, 2023)
12-14806475-A-G		not specified	Uncertain significance (Aug 12, 2021)
12-14806581-C-T		not specified	Uncertain significance (Aug 02, 2022)
12-14806619-A-G		not specified	Uncertain significance (Nov 07, 2022)
12-14806656-G-A		not specified	Uncertain significance (Sep 26, 2023)
12-14806671-T-C		not specified	Uncertain significance (Jul 11, 2023)
12-14823510-A-G		not specified	Uncertain significance (Aug 13, 2021)
12-14823542-C-A		not specified	Likely benign (Jul 06, 2021)
12-14829402-C-T		not specified	Uncertain significance (Jun 16, 2024)
12-14829418-G-C		ART4-related disorder	Benign (Oct 21, 2019)
12-14829445-T-G		not specified	Uncertain significance (Aug 14, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf60	protein_coding	protein_coding	ENST00000330828	1	103015

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0483	0.699	125679	0	28	125707	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0111	125	125	1.00	0.00000562	1650
Missense in Polyphen		18	23.488	0.76636		366
Synonymous	-0.700	49	43.2	1.14	0.00000201	442
Loss of Function	0.633	2	3.23	0.620	1.33e-7	53

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.000639	0.000621
Other	0.000330	0.000326

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.723
• rvis_EVS: 0.42
• rvis_percentile_EVS: 76.81

Haploinsufficiency Scores

• pHI: 0.0529
• hipred: N
• hipred_score: 0.146

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: BC049715