C12orf4

Rationale: 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

Refs: 25558065; 27311568; 28097321

Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to C12orf4 variants in ClinVar

2 Conditions Cataloged

not providedTotal: 3

Intellectual disability, autosomal recessive 66Total: 3

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript . Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				5 clinvar		5
missense		1 clinvar	8 clinvar	1 clinvar		10
nonsense	4 clinvar	5 clinvar	1 clinvar			10
start loss						0
frameshift	2 clinvar	4 clinvar	1 clinvar			7
splice donor/acceptor (+/-2bp)		1 clinvar	1 clinvar			2
Total	6	11	11	6	0	34

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 0 of 0 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
No transcripts match your selected source or search query.

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

regulation of mast cell degranulation

Cellular Component

cytoplasm

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000261250
Coding exons: 13
Length: 50781
Individuals with no LoFs: 125685
Homozygous LoFs: 0
Heterozygous LoFs: 62
Defined: 125747
p: 0.000247

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.53	209	281	0.744	0.0000137	3632
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00026	0.00025	rare
Latino/Admixed American	0.00048	0.00043	rare
Ashkenazi Jewish	0.00031	0.00030	rare
East Asian	0.00017	0.00016	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00026	0.00025	rare
South Asian	0.00028	0.00026	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N

Gene Damage Prediction

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