NM_001199799.2(ILDR1):c.1137G>C (p.Glu379Asp) AND not specified

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jul 11, 2017
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:: RCV000602874.4

Allele description [Variation Report for NM_001199799.2(ILDR1):c.1137G>C (p.Glu379Asp)]

NM_001199799.2(ILDR1):c.1137G>C (p.Glu379Asp)

Gene:

ILDR1:immunoglobulin like domain containing receptor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

3q13.33

Genomic location:

Preferred name:

NM_001199799.2(ILDR1):c.1137G>C (p.Glu379Asp)

HGVS:

NC_000003.12:g.121993612C>G
NG_031870.1:g.33669G>C
NG_031870.2:g.71943G>C
NM_001199799.2:c.1137G>CMANE SELECT
NM_001199800.2:c.870G>C
NM_175924.4:c.1005G>C
NP_001186728.1:p.Glu379Asp
NP_001186729.1:p.Glu290Asp
NP_787120.1:p.Glu335Asp
LRG_1377t1:c.1137G>C
LRG_1377:g.71943G>C
LRG_1377p1:p.Glu379Asp
NC_000003.11:g.121712459C>G
NM_001199799.1:c.1137G>C

Protein change:

E290D

Links:

dbSNP: rs1553743343

NCBI 1000 Genomes Browser:

rs1553743343

Molecular consequence:

NM_001199799.2:c.1137G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_001199800.2:c.870G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_175924.4:c.1005G>C - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: AllHighlyPenetrant
Identifiers:: MedGen: CN169374

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000731744	Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	criteria provided, single submitter (LMM Criteria)	Uncertain significance (Jul 11, 2017)	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

SCV000731744

Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine

criteria provided, single submitter

(LMM Criteria)

Uncertain significance
(Jul 11, 2017)

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	not provided	1	1	not provided	not provided	not provided	clinical testing

Citations

PubMed

A systematic approach to assessing the clinical significance of genetic variants.

Duzkale H, Shen J, McLaughlin H, Alfares A, Kelly MA, Pugh TJ, Funke BH, Rehm HL, Lebo MS.

Clin Genet. 2013 Nov;84(5):453-63. doi: 10.1111/cge.12257.

PubMed [citation]

PMID:: 24033266
PMCID:: PMC3995020

Details of each submission

From Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine, SCV000731744.1

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

Description

Variant classified as Uncertain Significance - Favor Benign. The p.Glu379Asp var iant in ILDR1 has not been previously reported in individuals with hearing loss or in large population studies. The glutamic acid (Glu) at position 379 is not c onserved across mammals or evolutionary distant species, with 2 mammals (lesser Egyptian jerboa, star-nosed mole) having an aspartic acid (Asp), supporting that the change at this position may be tolerated. Additional computational predicti on tools suggest that this variant may not impact the protein, though this infor mation is not predictive enough to rule out pathogenicity. In summary, while the clinical significance of the p.Glu379Asp variant is uncertain, available data s uggest that it is more likely to be benign.

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

Last Updated: Dec 24, 2022

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