CERT1

ceramide transporter 1, the group of StAR related lipid transfer domain containing|Pleckstrin homology domain containing

Basic information

Region (hg38): 5:75356345-75512138

Previous symbols: [ "COL4A3BP" ]

Links

ENSG00000113163

∙ NCBI:10087 ∙ OMIM:604677 ∙ HGNC:2205 ∙ Uniprot:Q9Y5P4 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

intellectual disability, autosomal dominant 34 (Strong), mode of inheritance: AD
intellectual disability, autosomal dominant 34 (Definitive), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Neurodevelopmental disorder with hypotonia, speech delay, and dysmorphic facies	AD	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	25533962

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CERT1 gene.

not_provided (85 variants)
Inborn_genetic_diseases (57 variants)
Intellectual_disability,_autosomal_dominant_34 (24 variants)
not_specified (14 variants)
CERT1-related_disorder (10 variants)
COL4A3BP-related_disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CERT1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001379029.1. 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	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	25 clinvar	1 clinvar	28
missense	2 clinvar	9 clinvar	95 clinvar	14 clinvar		120
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	2	9	101	39	1

Highest pathogenic variant AF is 6.92886e-7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CERT1	protein_coding	protein_coding	ENST00000380494	18	143653

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.667	0.333	125736	0	10	125746	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.36	272	406	0.670	0.0000204	4899
Missense in Polyphen		52	132.93	0.39119		1620
Synonymous	-1.79	175	147	1.19	0.00000733	1458
Loss of Function	4.81	9	43.1	0.209	0.00000229	496

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000876	0.0000876
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000514	0.0000462
European (Non-Finnish)	0.0000463	0.0000439
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Shelters ceramides and diacylglycerol lipids inside its START domain and mediates the intracellular trafficking of ceramides and diacylglycerol lipids in a non-vesicular manner. {ECO:0000269|PubMed:14685229, ECO:0000269|PubMed:17591919, ECO:0000269|PubMed:18184806, ECO:0000269|PubMed:20036255}.;
Disease: DISEASE: Mental retardation, autosomal dominant 34 (MRD34) [MIM:616351]: A form of mental retardation, a disorder characterized by significantly below average general intellectual functioning associated with impairments in adaptive behavior and manifested during the developmental period. {ECO:0000269|PubMed:25356899, ECO:0000269|PubMed:25533962}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Sphingolipid Metabolism;Metabolism of lipids;Metabolism;Glycosphingolipid metabolism;Sphingolipid de novo biosynthesis;Sphingolipid metabolism (Consensus)

Recessive Scores

pRec: 0.0962

Intolerance Scores

loftool: 0.197
rvis_EVS: -0.6
rvis_percentile_EVS: 17.75

Haploinsufficiency Scores

pHI: 0.232
hipred: Y
hipred_score: 0.672
ghis: 0.585

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.879

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Col4a3bp
Phenotype: growth/size/body region phenotype; muscle phenotype; craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; skeleton phenotype; embryo phenotype; respiratory system phenotype; hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); 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); hearing/vestibular/ear phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); limbs/digits/tail phenotype; vision/eye phenotype; immune system phenotype;

Zebrafish Information Network

Gene name: col4a3bpa
Affected structure: head
Phenotype tag: abnormal
Phenotype quality: decreased size

Gene ontology

Biological process: cell morphogenesis;in utero embryonic development;heart morphogenesis;ceramide metabolic process;muscle contraction;immune response;endoplasmic reticulum organization;signal transduction;cell population proliferation;phosphorylation;sphingolipid biosynthetic process;response to endoplasmic reticulum stress;ER to Golgi ceramide transport;ceramide transport;lipid homeostasis;mitochondrion morphogenesis;intermembrane lipid transfer;intermembrane sphingolipid transfer;ceramide 1-phosphate transport
Cellular component: nucleoplasm;mitochondrion;endoplasmic reticulum membrane;Golgi apparatus;cytosol;membrane;perinuclear region of cytoplasm
Molecular function: protein binding;lipid binding;kinase activity;phosphatidylinositol-4-phosphate binding;ceramide binding;intermembrane ceramide transfer activity;ceramide 1-phosphate binding;ceramide 1-phosphate transporter activity