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NM_032492.4(JAGN1):c.11G>T (p.Arg4Leu) AND Autosomal recessive severe congenital neutropenia due to JAGN1 deficiency

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Feb 5, 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:
RCV001993442.6

Allele description [Variation Report for NM_032492.4(JAGN1):c.11G>T (p.Arg4Leu)]

NM_032492.4(JAGN1):c.11G>T (p.Arg4Leu)

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.11G>T (p.Arg4Leu)
HGVS:
  • NC_000003.12:g.9890733G>T
  • NG_041779.1:g.5147G>T
  • NM_001363890.1:c.-258G>T
  • NM_032492.4:c.11G>TMANE SELECT
  • NP_115881.3:p.Arg4Leu
  • LRG_1228t1:c.11G>T
  • LRG_1228:g.5147G>T
  • LRG_1228p1:p.Arg4Leu
  • NC_000003.11:g.9932417G>T
Protein change:
R4L
Links:
dbSNP: rs569985954
NCBI 1000 Genomes Browser:
rs569985954
Molecular consequence:
  • NM_001363890.1:c.-258G>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
  • NM_032492.4:c.11G>T - 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

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002255533Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Uncertain significance
(Feb 5, 2022) 		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, SCV002255533.3

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). 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. This variant has not been reported in the literature in individuals affected with JAGN1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces arginine, which is basic and polar, with leucine, which is neutral and non-polar, at codon 4 of the JAGN1 protein (p.Arg4Leu).

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

Last Updated: Sep 29, 2024