C12orf43

chromosome 12 open reading frame 43

Basic information

Region (hg38): 12:121000486-121016502

Links

ENSG00000157895 ∙ NCBI:64897 ∙ ∙ HGNC:25719 ∙ Uniprot:Q96C57 ∙ 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 C12orf43 gene.

• Monogenic diabetes (2 variants)
• not provided (1 variants)
• Maturity-onset diabetes of the young type 3 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf43 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			3	1		4
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	2	5	20	10	15	52
Total	2	5	23	11	15

Variants in C12orf43

This is a list of pathogenic ClinVar variants found in the C12orf43 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-121000906-G-GTT			Benign (Jun 26, 2018)
12-121001041-T-C			Benign (Jun 14, 2018)
12-121001053-TTGCCTCTGCAG-T		Monogenic diabetes	Likely pathogenic (Oct 13, 2024)
12-121001057-C-T			Likely benign (Jul 29, 2023)
12-121001062-C-T			Conflicting classifications of pathogenicity (May 05, 2020)
12-121001064-G-A		Monogenic diabetes	Uncertain significance (May 04, 2022)
12-121001065-T-C		Maturity onset diabetes mellitus in young • 6 conditions	Uncertain significance/Uncertain risk allele (Apr 23, 2024)
12-121001066-G-A			Likely benign (Nov 17, 2023)
12-121001067-TCC-T		Monogenic diabetes	Likely pathogenic (Apr 17, 2022)
12-121001070-T-C		6 conditions	Uncertain significance (Mar 02, 2024)
12-121001074-G-C		Monogenic diabetes • 6 conditions	Uncertain significance (May 09, 2022)
12-121001076-A-C		Monogenic diabetes	Uncertain significance (Apr 18, 2022)
12-121001076-A-G		Monogenic diabetes	Benign (Jul 01, 2022)
12-121001077-G-T		Maturity-onset diabetes of the young type 3 • Monogenic diabetes • Maturity onset diabetes mellitus in young	Pathogenic (Jul 01, 2022)
12-121001080-TG-T		Keratoderma-ichthyosis-deafness syndrome, autosomal recessive • Monogenic diabetes	Likely pathogenic (Jul 01, 2022)
12-121001084-G-A			Likely benign (Mar 01, 2023)
12-121001085-C-T		6 conditions	Uncertain significance (Jun 18, 2024)
12-121001087-G-A			Likely benign (Feb 14, 2023)
12-121001096-C-T		Maturity-onset diabetes of the young type 3 • not specified • Maturity onset diabetes mellitus in young	Benign/Likely benign (Dec 22, 2023)
12-121001097-TC-T		Monogenic diabetes	Likely pathogenic (May 04, 2022)
12-121001098-C-CA		Monogenic diabetes	Uncertain significance (May 04, 2022)
12-121001106-A-G		6 conditions	Uncertain significance (May 04, 2024)
12-121001108-C-G		6 conditions	Uncertain significance (Dec 27, 2023)
12-121001112-G-A		Monogenic diabetes • Maturity-onset diabetes of the young type 3	Benign (Apr 17, 2022)
12-121001113-G-GC		Maturity-onset diabetes of the young type 3 • Monogenic diabetes • Maturity onset diabetes mellitus in young	Uncertain significance (May 04, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf43	protein_coding	protein_coding	ENST00000288757	6	14081

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000105	0.602	125736	0	11	125747	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.490	134	151	0.888	0.00000825	1695
Missense in Polyphen		27	36.365	0.74248		457
Synonymous	-0.564	67	61.4	1.09	0.00000371	506
Loss of Function	0.692	7	9.27	0.755	4.79e-7	103

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000904	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000352	0.0000352
Middle Eastern	0.0000544	0.0000544
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in the regulation of Wnt signaling pathway during early development. {ECO:0000250|UniProtKB:A9C3N6}.

Intolerance Scores

• loftool: 0.781
• rvis_EVS: 0.26
• rvis_percentile_EVS: 70.44

Haploinsufficiency Scores

• pHI: 0.130
• hipred: N
• hipred_score: 0.146
• ghis: 0.477

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: 2210016L21Rik

Zebrafish Information Network

• Gene name: zgc:162025
• Affected structure: head
• Phenotype tag: abnormal
• Phenotype quality: decreased size