NM_022072.5(NSUN3):c.454T>A (p.Cys152Ser) AND Combined oxidative phosphorylation deficiency 48

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Sep 17, 2020
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:: RCV001256013.1

Allele description [Variation Report for NM_022072.5(NSUN3):c.454T>A (p.Cys152Ser)]

NM_022072.5(NSUN3):c.454T>A (p.Cys152Ser)

Gene:

NSUN3:NOP2/Sun RNA methyltransferase 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q11.2

Genomic location:

Preferred name:

NM_022072.5(NSUN3):c.454T>A (p.Cys152Ser)

HGVS:

NC_000003.12:g.94084438T>A
NM_022072.5:c.454T>AMANE SELECT
NP_071355.1:p.Cys152Ser
NC_000003.11:g.93803282T>A

Protein change:

C152S; CYS152SER

Links:

OMIM: 617491.0003; dbSNP: rs2077284206

NCBI 1000 Genomes Browser:

rs2077284206

Molecular consequence:

NM_022072.5:c.454T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Combined oxidative phosphorylation deficiency 48
Identifiers:: MONDO: MONDO:0033566; MedGen: C5436602; OMIM: 619012

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001432790	OMIM	no assertion criteria provided	Pathogenic (Sep 17, 2020)	germline	literature only	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001432790

OMIM

no assertion criteria provided

Pathogenic
(Sep 17, 2020)

germline

literature only

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Correction to: Novel Biallelic NSUN3 Variants Cause Early-Onset Mitochondrial Encephalomyopathy and Seizures.

Paramasivam A, Meena AK, Venkatapathi C, Pitceathly RDS, Thangaraj K.

J Mol Neurosci. 2020 Dec;70(12):1966. doi: 10.1007/s12031-020-01652-2.

PubMed [citation]

PMID:: 32671698
PMCID:: PMC7658060

Details of each submission

From OMIM, SCV001432790.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In an 8-month-old boy, born of consanguineous East Asian parents, with combined oxidative phosphorylation deficiency-48 (COXPD48; 619012), Paramasivam et al. (2020) identified compound heterozygous missense mutations in exon 3 of the NSUN3 gene: a c.454T-A transversion, resulting in a cys152-to-ser (C152S) substitution, and a c.421G-C transversion, resulting in an ala141-to-pro (A141P; 617491.0004) substitution. The mutations, which were found by targeted sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Both occurred at highly conserved residues in the protein and neither were present in several public databases, including gnomAD. Functional studies of the variant and studies of patient cells were not performed.

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	not provided	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 23, 2022

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