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NM_032492.4(JAGN1):c.346A>G (p.Ile116Val) AND Autosomal recessive severe congenital neutropenia due to JAGN1 deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 8, 2020
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:
RCV001303464.4

Allele description [Variation Report for NM_032492.4(JAGN1):c.346A>G (p.Ile116Val)]

NM_032492.4(JAGN1):c.346A>G (p.Ile116Val)

Gene:
JAGN1:jagunal homolog 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3p25.3
Genomic location:
Preferred name:
NM_032492.4(JAGN1):c.346A>G (p.Ile116Val)
HGVS:
  • NC_000003.12:g.9893171A>G
  • NG_041779.1:g.7585A>G
  • NM_001363890.1:c.184A>G
  • NM_032492.4:c.346A>GMANE SELECT
  • NP_001350819.1:p.Ile62Val
  • NP_115881.3:p.Ile116Val
  • LRG_1228t1:c.346A>G
  • LRG_1228:g.7585A>G
  • LRG_1228p1:p.Ile116Val
  • NC_000003.11:g.9934855A>G
Protein change:
I116V
Links:
dbSNP: rs1467031121
NCBI 1000 Genomes Browser:
rs1467031121
Molecular consequence:
  • NM_001363890.1:c.184A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_032492.4:c.346A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Autosomal recessive severe congenital neutropenia due to JAGN1 deficiency
Synonyms:
Severe congenital neutropenia 6, autosomal recessive
Identifiers:
MONDO: MONDO:0014456; MedGen: C4014954; Orphanet: 423384; OMIM: 616022

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV001492711Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Jan 8, 2020) 		germlineclinical testing

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

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Citations

PubMed

Nothing to display

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001492711.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

This variant has not been reported in the literature in individuals with JAGN1-related conditions. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated, but these predictions have not been confirmed by published functional studies and their clinical significance is uncertain. This variant is not present in population databases (ExAC no frequency). This sequence change replaces isoleucine with valine at codon 116 of the JAGN1 protein (p.Ile116Val). The isoleucine residue is highly conserved and there is a small physicochemical difference between isoleucine and valine.

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

Last Updated: Sep 29, 2024