NM_003640.5(ELP1):c.3592C>T (p.Arg1198Ter) AND Familial dysautonomia

Germline classification:: Pathogenic/Likely pathogenic (2 submissions)
Last evaluated:: Dec 21, 2021
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:: RCV000668488.2

Allele description [Variation Report for NM_003640.5(ELP1):c.3592C>T (p.Arg1198Ter)]

NM_003640.5(ELP1):c.3592C>T (p.Arg1198Ter)

Gene:

ELP1:elongator acetyltransferase complex subunit 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q31.3

Genomic location:

Preferred name:

NM_003640.5(ELP1):c.3592C>T (p.Arg1198Ter)

HGVS:

NC_000009.12:g.108878731G>A
NG_008788.1:g.60598C>T
NM_001318360.2:c.3250C>T
NM_001330749.2:c.2545C>T
NM_003640.5:c.3592C>TMANE SELECT
NP_001305289.1:p.Arg1084Ter
NP_001317678.1:p.Arg849Ter
NP_003631.2:p.Arg1198Ter
LRG_251t1:c.3592C>T
LRG_251:g.60598C>T
NC_000009.11:g.111641011G>A
NM_003640.3:c.3592C>T
NM_003640.4:c.3592C>T

Protein change:

R1084*

Links:

dbSNP: rs376078668

NCBI 1000 Genomes Browser:

rs376078668

Molecular consequence:

NM_001318360.2:c.3250C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001330749.2:c.2545C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_003640.5:c.3592C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Familial dysautonomia (HSAN3)
Synonyms:: NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE III; HSAN III; Hereditary sensory and autonomic neuropathy 3; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009131; MedGen: C0013364; Orphanet: 1764; OMIM: 223900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000793101	Counsyl	criteria provided, single submitter (Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))	Likely pathogenic (Jul 27, 2017)	unknown	clinical testing	Citation Link,
SCV002096964	Baylor Genetics - CSER-TexasKidsCanSeq	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Dec 21, 2021)	maternal	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

SCV000793101

Counsyl

criteria provided, single submitter

(Counsyl Autosomal Recessive and X-Linked Classification Criteria (2018))

Likely pathogenic
(Jul 27, 2017)

unknown

clinical testing

Citation Link,

SCV002096964

Baylor Genetics - CSER-TexasKidsCanSeq

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Dec 21, 2021)

maternal

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	maternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical 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 Counsyl, SCV000793101.1

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

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

From Baylor Genetics - CSER-TexasKidsCanSeq, SCV002096964.1

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

Description

This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868].

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

Last Updated: Sep 29, 2024

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