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NM_003491.4(NAA10):c.109T>C (p.Ser37Pro) AND Ogden syndrome

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Jul 15, 2011
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV000022818.27

Allele description [Variation Report for NM_003491.4(NAA10):c.109T>C (p.Ser37Pro)]

NM_003491.4(NAA10):c.109T>C (p.Ser37Pro)

Gene:
NAA10:N-alpha-acetyltransferase 10, NatA catalytic subunit [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xq28
Genomic location:
Preferred name:
NM_003491.4(NAA10):c.109T>C (p.Ser37Pro)
HGVS:
  • NC_000023.11:g.153934388A>G
  • NG_012522.1:g.15392T>C
  • NG_031987.1:g.5767T>C
  • NM_001256119.2:c.109T>C
  • NM_001256120.2:c.109T>C
  • NM_003491.4:c.109T>CMANE SELECT
  • NP_001243048.1:p.Ser37Pro
  • NP_001243049.1:p.Ser37Pro
  • NP_003482.1:p.Ser37Pro
  • NC_000023.10:g.153199841A>G
  • NM_003491.3:c.109T>C
  • P41227:p.Ser37Pro
Protein change:
S37P; SER37PRO
Links:
NAA10 @ LOVD: NAA10_000008; UniProtKB: P41227#VAR_066652; OMIM: 300013.0001; dbSNP: rs387906701
NCBI 1000 Genomes Browser:
rs387906701
Molecular consequence:
  • NM_001256119.2:c.109T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001256120.2:c.109T>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003491.4:c.109T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Ogden syndrome (OGDNS)
Synonyms:
N-terminal acetyltransferase deficiency
Identifiers:
MONDO: MONDO:0010457; MedGen: C3275447; Orphanet: 276432; OMIM: 300855

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000044107OMIM
no assertion criteria provided
Pathogenic
(Jul 15, 2011)
germlineliterature only

PubMed (2)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlinenot providednot providednot providednot providednot providednot providedliterature only

Citations

PubMed

Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency.

Rope AF, Wang K, Evjenth R, Xing J, Johnston JJ, Swensen JJ, Johnson WE, Moore B, Huff CD, Bird LM, Carey JC, Opitz JM, Stevens CA, Jiang T, Schank C, Fain HD, Robison R, Dalley B, Chin S, South ST, Pysher TJ, Jorde LB, et al.

Am J Hum Genet. 2011 Jul 15;89(1):28-43. doi: 10.1016/j.ajhg.2011.05.017. Epub 2011 Jun 23. Erratum in: Am J Hum Genet. 2011 Aug 12;89(2):345.

PubMed [citation]
PMID:
21700266
PMCID:
PMC3135802

Biochemical and cellular analysis of Ogden syndrome reveals downstream Nt-acetylation defects.

Myklebust LM, Van Damme P, Støve SI, Dörfel MJ, Abboud A, Kalvik TV, Grauffel C, Jonckheere V, Wu Y, Swensen J, Kaasa H, Liszczak G, Marmorstein R, Reuter N, Lyon GJ, Gevaert K, Arnesen T.

Hum Mol Genet. 2015 Apr 1;24(7):1956-76. doi: 10.1093/hmg/ddu611. Epub 2014 Dec 8.

PubMed [citation]
PMID:
25489052
PMCID:
PMC4355026

Details of each submission

From OMIM, SCV000044107.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedliterature only PubMed (2)

Description

Rope et al. (2011) identified 2 unrelated families segregating a lethal X-linked disorder, Ogden syndrome (OGDNS; 300855). The 2 families had independent occurrences of a T-to-C transition at nucleotide 109 of the NAA10 gene, resulting in a serine-to-proline substitution at codon 37 (S37P). The NAA10 gene encodes the catalytic subunit of the N-terminal acetyltransferase. Substitution of proline for serine at position 37 is likely to affect structure, and in vitro assays of protein function demonstrated 60 to 80% reduction in NAT activity of the mutant protein toward the in vivo substrate RNase P protein p30 (606115). In contrast, the activity toward the substrate high mobility group protein A1 (600701) was reduced by only 20%.

Using structural modeling and simulations, Myklebust et al. (2015) found that S37P mutant NAA10 differs from wildtype NAA10 in regions involved in catalysis and at the interface between NAA10 and NAA15. The S37P mutation shortens helix alpha-2, weakens the interfacial hydrogen-bonding network, and reduces NAA10 flexibility. In vitro biochemical analysis demonstrated reduced substrate binding and catalytic capacity and impaired interaction between S37P mutant NAA10 and NAA15 (608000) or NAA50 (610834). Analysis of total protein N-acetylation in immortalized wildtype and Ogden syndrome B cells and fibroblasts revealed decreased acetylation of a subset of NatA and NatE substrates in Ogden syndrome cells. Furthermore, Ogden syndrome fibroblasts showed reduced cell migration and proliferation capacity, and elevated sensitivity to cell stresses.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlinenot providednot providednot providednot providednot providednot providednot providednot provided

Last Updated: Jan 7, 2023