NM_002951.5(RPN2):c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT AND Congenital disorder of glycosylation

Germline classification:: Likely benign (1 submission)
Last evaluated:: Jan 31, 2024
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:: RCV001443516.6

Allele description [Variation Report for NM_002951.5(RPN2):c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT]

NM_002951.5(RPN2):c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT

Genes:

MROH8:maestro heat like repeat family member 8 [Gene - HGNC]
RPN2:ribophorin II [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

20q11.23

Genomic location:

Preferred name:

NM_002951.5(RPN2):c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT

HGVS:

NC_000020.11:g.37179390_37179391insATAGACAGGGCCCCGCGGCCGGCACTCTT
NG_033795.2:g.5162_5190dup
NG_042268.1:g.5338_5339insATAGACAGGGCCCCGCGGCCGGCACTCTT
NG_142984.1:g.603_604insATAGACAGGGCCCCGCGGCCGGCACTCTT
NG_142985.1:g.43_44insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001135771.3:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001324299.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001324301.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001324302.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001324303.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001324304.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001324305.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_001324306.2:c.-187+21_-187+22insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_002951.5:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTTMANE SELECT
NM_152503.8:c.90_91insAAGAGTGCCGGCCGCGGGGCCCTGTCTATMANE SELECT
NM_213631.3:c.94_122dup
NM_213632.3:c.94_122dup
NP_689716.4:p.Ser41Argfs
NP_689716.4:p.Ser41Argfs
NP_689716.4:p.Ser41delinsArgValProAlaAlaGlyProCysLeuTer
NP_998796.1:p.Ser41delinsArgValProAlaAlaGlyProCysLeuTer
NP_998797.2:p.Ser41delinsArgValProAlaAlaGlyProCysLeuTer
NC_000020.10:g.35807790_35807791insCTTATAGACAGGGCCCCGCGGCCGGCACT
NC_000020.10:g.35807793_35807794insATAGACAGGGCCCCGCGGCCGGCACTCTT
NM_152503.6:c.90_91insAAGAGTGCCGGCCGCGGGGCCCTGTCTAT
NM_152503.7:c.94_122dup

Links:

dbSNP: rs11467214

NCBI 1000 Genomes Browser:

rs11467214

Molecular consequence:

NM_152503.8:c.90_91insAAGAGTGCCGGCCGCGGGGCCCTGTCTAT - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001135771.3:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001324299.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001324301.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001324302.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001324303.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001324304.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001324305.2:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_001324306.2:c.-187+21_-187+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_002951.5:c.13+21_13+22insATAGACAGGGCCCCGCGGCCGGCACTCTT - intron variant - [Sequence Ontology: SO:0001627]
NM_213631.3:c.94_122dup - nonsense - [Sequence Ontology: SO:0001587]
NM_213632.3:c.94_122dup - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Congenital disorder of glycosylation (CDG)
Synonyms:: Carbohydrate-deficient glycoprotein syndrome; Congenital disorders of glycosylation
Identifiers:: MONDO: MONDO:0015286; MedGen: C0282577; Orphanet: 137

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001646489	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 31, 2024)	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

SCV001646489

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 31, 2024)

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	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001646489.4

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

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

Last Updated: Feb 28, 2024

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