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NM_000501.4(ELN):c.1621C>T (p.Arg541Ter) AND ELN-related condition

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Oct 31, 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:
RCV003390688.4

Allele description

NM_000501.4(ELN):c.1621C>T (p.Arg541Ter)

Genes:
ELN-AS1:ELN antisense RNA 1 [Gene - HGNC]
ELN:elastin [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
7q11.23
Genomic location:
Preferred name:
NM_000501.4(ELN):c.1621C>T (p.Arg541Ter)
Other names:
p.R541*:CGA>TGA
HGVS:
  • NC_000007.14:g.74060184C>T
  • NG_009261.1:g.37088C>T
  • NM_000501.4:c.1621C>TMANE SELECT
  • NM_001081752.3:c.1534C>T
  • NM_001081753.3:c.1579C>T
  • NM_001081754.3:c.1636C>T
  • NM_001081755.3:c.1564C>T
  • NM_001278912.2:c.1621C>T
  • NM_001278913.2:c.1378C>T
  • NM_001278914.2:c.1549C>T
  • NM_001278915.2:c.1639C>T
  • NM_001278916.2:c.1477+137C>T
  • NM_001278917.2:c.1591C>T
  • NM_001278918.2:c.1354C>T
  • NM_001278939.2:c.1708C>T
  • NP_000492.2:p.Arg541Ter
  • NP_001075221.1:p.Arg512Ter
  • NP_001075222.1:p.Arg527Ter
  • NP_001075223.1:p.Arg546Ter
  • NP_001075224.1:p.Arg522Ter
  • NP_001265841.1:p.Arg541Ter
  • NP_001265842.1:p.Arg460Ter
  • NP_001265843.1:p.Arg517Ter
  • NP_001265844.1:p.Arg547Ter
  • NP_001265846.1:p.Arg531Ter
  • NP_001265847.1:p.Arg452Ter
  • NP_001265868.1:p.Arg570Ter
  • NC_000007.13:g.73474514C>T
  • NM_000501.2:c.1621C>T
  • NM_000501.3:c.1621C>T
  • NM_001278917.1:c.1591C>T
Nucleotide change:
1621C-T
Protein change:
R452*; ARG570TER
Links:
OMIM: 130160.0004; OMIM: 130160.0019; dbSNP: rs137854453
NCBI 1000 Genomes Browser:
rs137854453
Molecular consequence:
  • NM_001278916.2:c.1477+137C>T - intron variant - [Sequence Ontology: SO:0001627]
  • NM_000501.4:c.1621C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001081752.3:c.1534C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001081753.3:c.1579C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001081754.3:c.1636C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001081755.3:c.1564C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278912.2:c.1621C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278913.2:c.1378C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278914.2:c.1549C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278915.2:c.1639C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278917.2:c.1591C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278918.2:c.1354C>T - nonsense - [Sequence Ontology: SO:0001587]
  • NM_001278939.2:c.1708C>T - nonsense - [Sequence Ontology: SO:0001587]
Functional consequence:
effect on RNA splicing [PubMedVariation Ontology: 0362]

Condition(s)

Name:
ELN-related condition
Identifiers:

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004119759PreventionGenetics, part of Exact Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)		Pathogenic
(Oct 31, 2022) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot 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 PreventionGenetics, part of Exact Sciences, SCV004119759.1

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

Description

The ELN c.1621C>T variant is predicted to result in premature protein termination (p.Arg541*). In an alternate transcript (NM_00127893.2) this variant is referred to as c.1708C>T (p.Arg570*). This variant has been reported in multiple individuals with ELN-related disease and in at least one individual it was reported to occur de novo (see for example - Li et al. 1997. PubMed ID: 9215670; Table S9 - Jin et al. 2017. PubMed ID: 28991257). This variant has not been reported in a large population database (http://gnomad.broadinstitute.org), indicating this variant is rare. Nonsense variants in ELN are expected to be pathogenic. This variant is interpreted as pathogenic.

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

Last Updated: Mar 10, 2024