Human Gene Module / Chromosome X / NAA10

NAA10N-alpha-acetyltransferase 10, NatA catalytic subunit

SFARI Gene Score
3S
Suggestive Evidence, Syndromic Criteria 3.1, Syndromic
Autism Reports / Total Reports
3 / 13
Rare Variants / Common Variants
45 / 0
Aliases
-
Associated Syndromes
Ogden syndrome, DD, ID, epilepsy/seizures, Ogden syndrome, DD, ID, Ogden syndrome, ASD, DD, epilepsy/seizures, Ogden syndrome, DD, epilepsy/seizures
Chromosome Band
Xq28
Associated Disorders
-
Relevance to Autism

Mutations in the NAA10 gene are responsible for Ogden syndrome (OMIM 300855), an X-linked neurodevelopmental disorder characterized by postnatal growth failure, severely delayed psychomotor development, variable dysmorphic features, and hypotonia; a subset of individuals with this syndrome have also presented with autism spectrum disorder or autistic features/stereotypy (Popp et al., 2015; Saunier et al., 2016; Sidhu et al., 2017; Valentine et al., 2018; Cheng et al., 2019; Bader et al., 2020; Maini et al., 2021; McTiernan et al., 2022; Lyon et al., 2023). Mutations in this gene are also responsible for a syndromic form of microphthalmia (MCOPS1; OMIM 309800), an X-linked disorder characterized by unilateral or bilateral microphthalmia or anophthalmia with frequently observed extraocular features that include impaired intellectual development, large and dysplastic ears with skin tags, high-arched or cleft palate, dental anomalies, urogenital anomalies, and skeletal manifestations including lordosis or scoliosis, clinodactyly, syndactyly, brachydactyly, and abnormal thumbs; worsening autistic behavior was observed in one of three brothers with this condition who had a maternally-inherited splice-site variant in the NAA10 gene (Esmailpour et al., 2014). Missense variants in the NAA10 gene have also been identified in ASD probands from WES/WGS studies (Mahjani et al., 2021; Chan et al., 2022).

Molecular Function

N-alpha-acetylation is among the most common post-translational protein modifications in eukaryotic cells. This process involves the transfer of an acetyl group from acetyl-coenzyme A to the alpha-amino group on a nascent polypeptide and is essential for normal cell function. This gene encodes an N-terminal acetyltransferase that functions as the catalytic subunit of the major amino-terminal acetyltransferase A complex.

SFARI Genomic Platforms
Reports related to NAA10 (13 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support - Esmailpour T et al. (2014) No Autistic behavior, epilepsy/seizures
2 Support - Popp B et al. (2015) No Autistic features, stereotypy
3 Support - Casey JP et al. (2015) No -
4 Support - Saunier C et al. (2016) No ADHD, epilepsy/seizures, stereotypy
5 Support - Sidhu M et al. (2017) Yes -
6 Support - Valentine V et al. (2018) No Stereotypy
7 Support Phenotypic and biochemical analysis of an international cohort of individuals with variants in NAA10 and NAA15 Cheng H , et al. (2019) No ASD or autistic features, ADHD, epilepsy/seizures,
8 Support - Bader I et al. (2020) No Stereotypy
9 Support - Maini I et al. (2021) No Stereotypy
10 Support - Mahjani B et al. (2021) Yes -
11 Support - McTiernan N et al. (2022) No Autistic features
12 Support - Chan AJS et al. (2022) Yes -
13 Primary - Lyon GJ et al. (2023) No ASD, ADHD, epilepsy/seizures, stereotypy
Rare Variants   (45)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
c.22C>T p.Pro8Ser missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.30C>G p.Asp10Glu missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.47A>C p.His16Pro missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.92A>G p.Tyr31Cys missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.247C>T p.Arg83Cys missense_variant De novo - - 28967461 Sidhu M et al. (2017)
c.247C>T p.Arg83Cys missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.29A>G p.Asp10Gly missense_variant De novo - - 31127942 Cheng H , et al. (2019)
c.359A>C p.His120Pro missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.367T>C p.Ser123Pro missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.383T>C p.Phe128Ser missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.384T>G p.Phe128Leu missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.440T>C p.Met147Thr missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.445C>T p.Arg149Trp missense_variant De novo - - 37130971 Lyon GJ et al. (2023)
c.247C>T p.Arg83Cys missense_variant De novo - - 31127942 Cheng H , et al. (2019)
c.259G>T p.Ala87Ser missense_variant De novo - - 31127942 Cheng H , et al. (2019)
c.311C>A p.Ala104Asp missense_variant De novo - - 31127942 Cheng H , et al. (2019)
c.361C>G p.Leu121Val missense_variant De novo - - 31127942 Cheng H , et al. (2019)
c.361C>G p.Leu121Val missense_variant Unknown - - 31127942 Cheng H , et al. (2019)
c.384T>G p.Phe128Leu missense_variant De novo - - 31127942 Cheng H , et al. (2019)
c.440T>C p.Met147Thr missense_variant De novo - - 31127942 Cheng H , et al. (2019)
c.346C>G p.Arg116Gly missense_variant De novo - - 36309498 Chan AJS et al. (2022)
c.247C>T p.Arg83Cys missense_variant De novo - - 27094817 Saunier C et al. (2016)
c.247C>T p.Arg83Cys missense_variant Unknown - - 34615535 Mahjani B et al. (2021)
c.346C>T p.Arg116Trp missense_variant De novo - - 27094817 Saunier C et al. (2016)
c.382T>A p.Phe128Ile missense_variant De novo - - 27094817 Saunier C et al. (2016)
c.384T>A p.Phe128Leu missense_variant De novo - - 27094817 Saunier C et al. (2016)
c.47A>C p.His16Pro missense_variant De novo - Simplex 32698785 Bader I et al. (2020)
c.319G>T p.Val107Phe missense_variant De novo - Simplex 25099252 Popp B et al. (2015)
c.346C>T p.Arg116Trp missense_variant De novo - Simplex 25099252 Popp B et al. (2015)
c.247C>T p.Arg83Cys missense_variant De novo - Simplex 34200686 Maini I et al. (2021)
c.215T>C p.Ile72Thr missense_variant Familial Maternal - 37130971 Lyon GJ et al. (2023)
c.215T>C p.Ile72Thr missense_variant Familial Maternal - 31127942 Cheng H , et al. (2019)
c.32T>G p.Leu11Arg missense_variant Unknown Not maternal - 31127942 Cheng H , et al. (2019)
c.346C>T p.Arg116Trp missense_variant De novo - Simplex 29957440 Valentine V et al. (2018)
c.384T>G p.Phe128Leu missense_variant De novo - Simplex 35039925 McTiernan N et al. (2022)
c.386A>C p.Gln129Pro missense_variant De novo - Simplex 35039925 McTiernan N et al. (2022)
c.16G>C p.Ala6Pro missense_variant Familial Maternal Simplex 35039925 McTiernan N et al. (2022)
c.426+2T>A - splice_site_variant Familial Maternal Multiplex 24431331 Esmailpour T et al. (2014)
c.128A>C p.Tyr43Ser missense_variant Familial Maternal Multiplex 26522270 Casey JP et al. (2015)
c.469G>A p.Glu157Lys missense_variant Familial Maternal Simplex 35039925 McTiernan N et al. (2022)
c.455_458del p.Thr152ArgfsTer6 frameshift_variant Familial Maternal - 37130971 Lyon GJ et al. (2023)
c.499_500del p.Ser167GlnfsTer23 frameshift_variant Familial Maternal - 37130971 Lyon GJ et al. (2023)
c.410_413del p.Thr137ArgfsTer6 frameshift_variant Familial Maternal Simplex 31127942 Cheng H , et al. (2019)
c.235C>T p.Arg79Cys missense_variant Familial Maternal Extended multiplex 35039925 McTiernan N et al. (2022)
c.247C>T p.Arg83Cys missense_variant De novo (germline mosaicism) - Multiplex 27094817 Saunier C et al. (2016)
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
icon
3S

Increased from to 3S

Krishnan Probability Score

Score 0.3270924461031

Ranking 25262/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.18842779969779

Ranking 7104/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.9120645792719

Ranking 7813/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score

Score -0.091376908953155

Ranking 12029/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
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