C12orf57

chromosome 12 open reading frame 57

Basic information

Region (hg38): 12:6942977-6946003

Links

ENSG00000111678 ∙ NCBI:113246 ∙ OMIM:615140 ∙ HGNC:29521 ∙ Uniprot:Q99622 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• temtamy syndrome (Strong), mode of inheritance: AR
• temtamy syndrome (Moderate), mode of inheritance: AR
• temtamy syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Temtamy syndrome	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Neurologic; Ophthalmologic	17632789; 21937992; 23453665; 23453666; 23633300; 24798461

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C12orf57 gene.

• Temtamy syndrome (186 variants)
• not provided (27 variants)
• not specified (12 variants)
• Inborn genetic diseases (6 variants)
• 6 conditions (1 variants)
• Intellectual disability (1 variants)
• Microphthalmia, isolated, with coloboma;Global developmental delay;Abnormal corpus callosum morphology;Seizure (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf57 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			2	45	1	48
missense			84			84
nonsense	2	2				4
start loss	1	1				2
frameshift	6	1	1			8
inframe indel			2			2
splice donor/acceptor (+/-2bp)	1	3	2			6
splice region			2	7		9
non coding			2	30	5	37
Total	10	7	93	75	6

Highest pathogenic variant AF is 0.0000131

Variants in C12orf57

This is a list of pathogenic ClinVar variants found in the C12orf57 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6943663-G-A		C12orf57-related disorder	Uncertain significance (Nov 21, 2023)
12-6943732-G-A			Likely benign (Mar 29, 2021)
12-6943738-G-GA			Likely benign (Apr 18, 2021)
12-6943745-G-T			Likely benign (Apr 13, 2021)
12-6943811-C-T			Benign (Mar 28, 2021)
12-6943813-C-T			Likely benign (Apr 11, 2021)
12-6943815-G-A			Benign (Mar 29, 2021)
12-6943838-T-G		Aicardi-Goutieres syndrome 9	Uncertain significance (Sep 02, 2022)
12-6943843-C-G		Aicardi-Goutieres syndrome 9	Likely pathogenic (Jul 28, 2021)
12-6943843-C-T		Aicardi-Goutieres syndrome 9	Pathogenic/Likely pathogenic (Oct 26, 2022)
12-6943845-A-G		Aicardi-Goutieres syndrome 9	Likely pathogenic (May 26, 2021)
12-6943846-G-C			Uncertain significance (Sep 01, 2022)
12-6943848-AGGCTTTCT-A		Aicardi-Goutieres syndrome 9	Likely pathogenic (Oct 01, 2023)
12-6943850-G-A		Aicardi-Goutieres syndrome 9	Pathogenic (Aug 16, 2021)
12-6943851-C-T			Benign/Likely benign (Feb 01, 2024)
12-6943852-T-G			Uncertain significance (Sep 01, 2022)
12-6943856-T-C			Likely benign (Aug 01, 2023)
12-6943856-T-G		Aicardi-Goutieres syndrome 9	Pathogenic (Aug 16, 2021)
12-6943859-C-T		not specified	Benign (Jan 24, 2024)
12-6943863-T-C			Benign (Mar 28, 2021)
12-6943864-T-C			Likely benign (Jan 01, 2024)
12-6943866-C-T		Aicardi-Goutieres syndrome 9	Benign/Likely benign (Aug 01, 2023)
12-6943867-C-T			Likely benign (Mar 29, 2021)
12-6943875-C-T			Likely benign (Apr 02, 2021)
12-6943881-T-C			Likely benign (Apr 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf57	protein_coding	protein_coding	ENST00000229281	3	3026

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000524	0.267	125734	0	13	125747	0.0000517

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.897	102	79.5	1.28	0.00000419	811
Missense in Polyphen		28	26.549	1.0547		273
Synonymous	-2.56	55	35.6	1.55	0.00000210	261
Loss of Function	-0.331	6	5.19	1.16	2.22e-7	58

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000268	0.000268
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.0000656	0.0000653
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: In brain, may be required for corpus callusum development. {ECO:0000269|PubMed:23453666}.

Recessive Scores

• pRec: 0.109

Intolerance Scores

• loftool: 0.584
• rvis_EVS: -0.12
• rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

• pHI: 0.0468
• hipred: N
• hipred_score: 0.454
• ghis: 0.538

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: Grcc10
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: post-embryonic development;regulation of skeletal muscle contraction;corpus callosum morphogenesis;third ventricle development;psychomotor behavior;camera-type eye morphogenesis;cognition
• Cellular component: cytoplasm;nuclear speck
• Molecular function: molecular_function