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NM_001375380.1(EBF3):c.488G>T (p.Arg163Leu) AND not provided

Germline classification:
Pathogenic (2 submissions)
Last evaluated:
Oct 23, 2020
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000493860.4

Allele description [Variation Report for NM_001375380.1(EBF3):c.488G>T (p.Arg163Leu)]

NM_001375380.1(EBF3):c.488G>T (p.Arg163Leu)

Gene:
EBF3:EBF transcription factor 3 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
10q26.3
Genomic location:
Preferred name:
NM_001375380.1(EBF3):c.488G>T (p.Arg163Leu)
HGVS:
  • NC_000010.11:g.129957324C>A
  • NG_030038.1:g.11504G>T
  • NM_001005463.3:c.488G>T
  • NM_001375379.1:c.488G>T
  • NM_001375380.1:c.488G>TMANE SELECT
  • NM_001375389.1:c.488G>T
  • NM_001375390.1:c.488G>T
  • NM_001375391.1:c.488G>T
  • NM_001375392.1:c.488G>T
  • NP_001005463.1:p.Arg163Leu
  • NP_001362308.1:p.Arg163Leu
  • NP_001362309.1:p.Arg163Leu
  • NP_001362318.1:p.Arg163Leu
  • NP_001362319.1:p.Arg163Leu
  • NP_001362320.1:p.Arg163Leu
  • NP_001362321.1:p.Arg163Leu
  • NC_000010.10:g.131755588C>A
  • NM_001005463.2:c.488G>T
Protein change:
R163L; ARG163LEU
Links:
OMIM: 607407.0006; dbSNP: rs1057519389
NCBI 1000 Genomes Browser:
rs1057519389
Molecular consequence:
  • NM_001005463.3:c.488G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375379.1:c.488G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375380.1:c.488G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375389.1:c.488G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375390.1:c.488G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375391.1:c.488G>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001375392.1:c.488G>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000581794GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Pathogenic
(May 4, 2017) 		germlineclinical testing

Citation Link,

SCV001446868Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 23, 2020) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot provided1not providedclinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From GeneDx, SCV000581794.3

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The R163L variant in the EBF3 gene has been reported previously as a de novo variant in a female child with global developmental delay, congenital hypotonia, torticollis, facial weakness, dysphagia, dysmorphic features including triangular facies, and a normal brain MRI (Chao et al., 2017). The R163L variant is not observed in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). The R163L variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species. In silico analysis predicts this variant is probably damaging to the protein structure/function. We interpret R163L as a pathogenic variant.

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

From Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen, SCV001446868.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyes1not providednot providednot providednot providednot providednot provided

Last Updated: Jul 15, 2024