Human Gene Module / Chromosome 5 / CERT1

CERT1ceramide transporter 1

SFARI Gene Score
3S
Suggestive Evidence, Syndromic Criteria 3.1, Syndromic
Autism Reports / Total Reports
5 / 8
Rare Variants / Common Variants
31 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
5q13.3
Associated Disorders
-
Relevance to Autism

De novo missense variants in the CERT1 gene have been identified in multiple ASD probands (De Rubeis et al., 2014; Iossifov et al., 2014; Takata et al., 2018; Zhou et al., 2022). Three male patients with impaired intellectual development from the Deciphering Developmental Disorders 2015 study were identified with the same de novo p.Ser132Leu missense variant in the CERT1 gene; one of these three patients also presented with stereotypic behavior. Gehin et al., 2023 characterized 31 unrelated individuals with 22 CERT1 missense variants presenting with a neurodevelopmental syndrome characterized by infantile hypotonia, mild dysmorphic features, variable degrees of intellectual disability, motor and speech delays, increased pain tolerance, and seizures; 19/27 (70%) of the individuals in this study were either diagnosed with autism spectrum disorder (ASD) or presented with possible ASD, and several of the CERT1 missense variants identified in affected individuals were experimentally shown to result in gain-of-function effects.

Molecular Function

This gene encodes a kinase that specifically phosphorylates the N-terminal region of the non-collagenous domain of the alpha 3 chain of type IV collagen, known as the Goodpasture antigen. Goodpasture disease is the result of an autoimmune response directed at this antigen. One isoform of this protein is also involved in ceramide intracellular transport.

SFARI Genomic Platforms
Reports related to CERT1 (8 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support Synaptic, transcriptional and chromatin genes disrupted in autism De Rubeis S , et al. (2014) Yes -
2 Support The contribution of de novo coding mutations to autism spectrum disorder Iossifov I et al. (2014) Yes -
3 Support Large-scale discovery of novel genetic causes of developmental disorders Deciphering Developmental Disorders Study (2014) No Stereotypy
4 Support Integrative Analyses of De Novo Mutations Provide Deeper Biological Insights into Autism Spectrum Disorder Takata A , et al. (2018) Yes -
5 Support - Zhou X et al. (2022) Yes -
6 Primary - Gehin C et al. (2023) Yes ADHD, epilepsy/seizures, stereotypy
7 Support - Sanchis-Juan A et al. (2023) No -
8 Support - Hosneara Akter et al. () No -
Rare Variants   (31)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.159G>A p.Trp53Ter stop_gained Unknown - - 39342494 Hosneara Akter et al. ()
c.676C>T p.Arg226Cys missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.1751A>G p.His584Arg missense_variant De novo - - 35982159 Zhou X et al. (2022)
c.663T>G p.Ser221Arg missense_variant Unknown - - 36976648 Gehin C et al. (2023)
c.779C>T p.Ser260Leu missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.787T>C p.Ser263Pro missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.797C>G p.Ser266Cys missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.805A>C p.Ser269Arg missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.880A>G p.Thr294Ala missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1111G>A p.Gly371Arg missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1112G>A p.Gly371Glu missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1124C>T p.Thr375Ile missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1135A>G p.Thr379Ala missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1256A>G p.Tyr419Cys missense_variant Unknown - - 36976648 Gehin C et al. (2023)
c.1271C>G p.Thr424Arg missense_variant Unknown - - 36976648 Gehin C et al. (2023)
c.1318G>C p.Gly440Arg missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1369G>C p.Ala457Pro missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1373T>C p.Leu458Pro missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1481G>C p.Arg494Thr missense_variant Unknown - - 36976648 Gehin C et al. (2023)
c.1525A>G p.Ile509Val missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1655A>G p.Glu552Gly missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.1883C>T p.Pro628Leu missense_variant De novo - - 36976648 Gehin C et al. (2023)
c.928T>C p.Phe310Leu missense_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.2238A>G p.Ala746= synonymous_variant De novo - - 25363760 De Rubeis S , et al. (2014)
c.998C>G p.Leu330Val missense_variant De novo - Simplex 36976648 Gehin C et al. (2023)
c.561T>G p.Asp187Glu missense_variant De novo - Simplex 29346770 Takata A , et al. (2018)
c.1360G>T p.Val454Phe missense_variant Familial Paternal - 36976648 Gehin C et al. (2023)
c.1730C>T p.Ala577Val missense_variant Familial Maternal - 36976648 Gehin C et al. (2023)
c.880A>G p.Thr294Ala missense_variant De novo - Simplex 25363768 Iossifov I et al. (2014)
c.517G>A p.Val173Ile missense_variant Unknown - Simplex 37541188 Sanchis-Juan A et al. (2023)
c.779C>T p.Ser260Leu missense_variant De novo - Simplex 25533962 Deciphering Developmental Disorders Study (2014)
Common Variants  

No common variants reported.

SFARI Gene score
3S

Suggestive Evidence, Syndromic

Score Delta: Score remained at 3S

3

Suggestive Evidence

See all Category 3 Genes

The literature is replete with relatively small studies of candidate genes, using either common or rare variant approaches, which do not reach the criteria set out for categories 1 and 2. Genes that had two such lines of supporting evidence were placed in category 3, and those with one line of evidence were placed in category 4. Some additional lines of "accessory evidence" (indicated as "acc" in the score cards) could also boost a gene from category 4 to 3.

The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."

7/1/2023
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3S

Increased from to 3S

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