NM_022162.3(NOD2):c.3019dup (p.Leu1007fs) AND not provided

Germline classification:: Conflicting interpretations of pathogenicity (4 submissions)
Last evaluated:: Oct 26, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001701717.22

Allele description [Variation Report for NM_022162.3(NOD2):c.3019dup (p.Leu1007fs)]

NM_022162.3(NOD2):c.3019dup (p.Leu1007fs)

Genes:

CYLD-AS1:CYLD antisense RNA 1 [Gene - HGNC]
NOD2:nucleotide binding oligomerization domain containing 2 [Gene - OMIM - HGNC]

Variant type:

Duplication

Cytogenetic location:

16q12.1

Genomic location:

Preferred name:

NM_022162.3(NOD2):c.3019dup (p.Leu1007fs)

HGVS:

NC_000016.10:g.50729870dup
NC_000016.9:g.50763781dupC
NG_007508.1:g.37732dup
NM_001293557.2:c.2938dup
NM_001370466.1:c.2938dupMANE SELECT
NM_022162.3:c.3019dup
NP_001280486.1:p.Leu980fs
NP_001357395.1:p.Leu980fs
NP_071445.1:p.Leu1007fs
LRG_177t1:c.3019dup
LRG_177:g.37732dup
NC_000016.9:g.50763778_50763779insC
NC_000016.9:g.50763781dup
NC_000016.9:g.50763781dup
NM_001370466.1:c.2938dup
NM_022162.1:c.3019dupC
NM_022162.2:c.3019dupC
NR_163434.1:n.3150dup

Protein change:

L1007fs

Links:

OMIM: 605956.0001; OMIM: 605956.0012; dbSNP: rs2066847

NCBI 1000 Genomes Browser:

rs2066847

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

Clear Turn Off Turn On

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

Help

Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001928554	Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV001973634	Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus See additional submitters Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen	no assertion criteria provided	Likely benign	germline	clinical testing
SCV002058052	ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories	criteria provided, single submitter (ARUP Molecular Germline Variant Investigation Process 2024)	Likely benign (Oct 26, 2023)	germline	clinical testing	Citation Link,
SCV002502239	AiLife Diagnostics, AiLife Diagnostics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Mar 31, 2022)	germline	clinical testing	PubMed (71) [See all records that cite these PMIDs] 11385577, 28422189, 19397946, 15002819, 12673278, 19641059, 17301648, 21335489, 12512038, 26167078, 16010583, 21951874, 21745302, 19185283, 30166421, 22543157, 32597225, 11910337, 16669960, 29867916, 28750667, 24047397, 21565239, 29248579, 23173613, 11425413, 30553995, 28658209, 29321258, 24345423, 23128233, 12704363, 22440928, 19748964, 23633568, 20713205, 27373512, 23709157, 12650796, 24586700, 22344438, 19103559, 16416181, 19184348, 19184350, 27306066, 29178652, 22275320, 19349988, 28008999, 29446656, 21548950, 18942754, 20332463, 21983784, 29795570, 26042516, 24597572, 30167848, 21994160, 32716958, 25365249, 20047977, 22684479, 21460759, 30552907, 17489054, 19713276, 23615072, 22939045, 25741868

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	11	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A frameshift mutation in NOD2 associated with susceptibility to Crohn's disease.

Ogura Y, Bonen DK, Inohara N, Nicolae DL, Chen FF, Ramos R, Britton H, Moran T, Karaliuskas R, Duerr RH, Achkar JP, Brant SR, Bayless TM, Kirschner BS, Hanauer SB, Nuñez G, Cho JH.

Nature. 2001 May 31;411(6837):603-6.

PubMed [citation]

PMID:: 11385577

Exome Analysis of Rare and Common Variants within the NOD Signaling Pathway.

Andreoletti G, Shakhnovich V, Christenson K, Coelho T, Haggarty R, Afzal NA, Batra A, Petersen BS, Mort M, Beattie RM, Ennis S.

Sci Rep. 2017 Apr 19;7:46454. doi: 10.1038/srep46454.

PubMed [citation]

PMID:: 28422189
PMCID:: PMC5396125

See all PubMed Citations (71)

Details of each submission

From Genome Diagnostics Laboratory, University Medical Center Utrecht - VKGL Data-share Consensus, SCV001928554.1

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

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

From Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center - VKGL Data-share Consensus, SCV001973634.1

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

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

From ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories, SCV002058052.6

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

#	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

From AiLife Diagnostics, AiLife Diagnostics, SCV002502239.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	11	not provided	not provided	clinical testing	PubMed (71)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	yes	not provided	not provided	not provided		11	not provided	not provided	not provided

Last Updated: Oct 13, 2024

ClinVar

Relating variation to medicine