C12orf4

chromosome 12 open reading frame 4

Basic information

Region (hg38): 12:4487734-4538508

Links

ENSG00000047621 ∙ NCBI:57102 ∙ OMIM:616082 ∙ HGNC:1184 ∙ Uniprot:Q9NQ89 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• intellectual disability, autosomal recessive 66 (Strong), mode of inheritance: AR
• intellectual disability, autosomal recessive 66 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Intellectual developmental disorder, autosomal recessive 66	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; Musculoskeletal; Neurologic	25558065; 27311568; 28097321

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the C12orf4 gene.

• not provided (3 variants)
• Intellectual disability, autosomal recessive 66 (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C12orf4 gene is commonly pathogenic or not. These statistics are base on transcript: . Only rare variants are included in the table.

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.

Effect	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous				5		5
missense		1	8	1		10
nonsense	4	5	1			10
start loss						0
frameshift	2	4	1			7
splice donor/acceptor (+/-2bp)		1	1			2
Total	6	11	11	6	0

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C12orf4	protein_coding	protein_coding	ENST00000261250	13	50781

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000107	0.999	125685	0	62	125747	0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	209	281	0.744	0.0000137	3632
Missense in Polyphen		53	102.8	0.51555		1296
Synonymous	2.75	64	98.7	0.648	0.00000475	991
Loss of Function	3.03	14	32.7	0.429	0.00000178	401

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000744	0.000726
Ashkenazi Jewish	0.000308	0.000298
East Asian	0.000169	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000261	0.000255
Middle Eastern	0.000169	0.000163
South Asian	0.000282	0.000261
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in mast cell degranulation. {ECO:0000250|UniProtKB:D4A770}.

Intolerance Scores

• loftool: 0.388
• rvis_EVS: -0.6
• rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.488
• ghis: 0.657

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: D6Wsu163e

Gene ontology

• Biological process: regulation of mast cell degranulation
• Cellular component: cytoplasm