NM_017755.6(NSUN2):c.1566del (p.Phe522fs) AND Intellectual disability, autosomal recessive 5

Germline classification:: Likely pathogenic (1 submission)
Last evaluated:: Sep 1, 2022
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV002283598.1

Allele description [Variation Report for NM_017755.6(NSUN2):c.1566del (p.Phe522fs)]

NM_017755.6(NSUN2):c.1566del (p.Phe522fs)

Gene:

NSUN2:NOP2/Sun RNA methyltransferase 2 [Gene - OMIM - HGNC]

Variant type:

Deletion

Cytogenetic location:

5p15.31

Genomic location:

Preferred name:

NM_017755.6(NSUN2):c.1566del (p.Phe522fs)

HGVS:

NC_000005.10:g.6606857del
NG_028215.1:g.31506del
NM_001193455.2:c.1461del
NM_017755.6:c.1566delMANE SELECT
NP_001180384.1:p.Phe487fs
NP_060225.4:p.Phe522fs
NC_000005.9:g.6606970del
NR_037947.2:n.1546del

Protein change:

F487fs

Molecular consequence:

NM_001193455.2:c.1461del - frameshift variant - [Sequence Ontology: SO:0001589]
NM_017755.6:c.1566del - frameshift variant - [Sequence Ontology: SO:0001589]
NR_037947.2:n.1546del - non-coding transcript variant - [Sequence Ontology: SO:0001619]

Observations:

Condition(s)

Name:: Intellectual disability, autosomal recessive 5 (MRT5)
Synonyms:: INTELLECTUAL DEVELOPMENTAL DISORDER, AUTOSOMAL RECESSIVE 5
Identifiers:: MONDO: MONDO:0012613; MedGen: C1970199; Orphanet: 88616; OMIM: 611091

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002572514	3billion	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Sep 1, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002572514

3billion

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Sep 1, 2022)

germline

clinical testing

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	yes	1	not provided	not provided	1	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From 3billion, SCV002572514.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	1	not provided	not provided	clinical testing	PubMed (1)

Description

The variant is not observed in the gnomAD v2.1.1 dataset. It is predicted to result in a loss or disruption of normal protein function through nonsense-mediated decay (NMD) or protein truncation. This variant is classified as Likely pathogenic according to the recommendation of ACMG/AMP guideline.

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

Last Updated: Aug 5, 2023

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