NM_003640.5(ELP1):c.3592C>T (p.Arg1198Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 18, 2023
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:: RCV001071602.5

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)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001236913	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 18, 2023)	germline	clinical testing	PubMed (3) [See all records that cite these PMIDs] 18303054, 24173031, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001236913

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 18, 2023)

germline

clinical testing

PubMed (3)
[See all records that cite these PMIDs]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

IKAP localizes to membrane ruffles with filamin A and regulates actin cytoskeleton organization and cell migration.

Johansen LD, Naumanen T, Knudsen A, Westerlund N, Gromova I, Junttila M, Nielsen C, Bøttzauw T, Tolkovsky A, Westermarck J, Coffey ET, Jäättelä M, Kallunki T.

J Cell Sci. 2008 Mar 15;121(Pt 6):854-64. doi: 10.1242/jcs.013722. Epub 2008 Feb 26.

PubMed [citation]

PMID:: 18303054

Familial dysautonomia model reveals Ikbkap deletion causes apoptosis of Pax3+ progenitors and peripheral neurons.

George L, Chaverra M, Wolfe L, Thorne J, Close-Davis M, Eibs A, Riojas V, Grindeland A, Orr M, Carlson GA, Lefcort F.

Proc Natl Acad Sci U S A. 2013 Nov 12;110(46):18698-703. doi: 10.1073/pnas.1308596110. Epub 2013 Oct 30.

PubMed [citation]

PMID:: 24173031
PMCID:: PMC3831979

See all PubMed Citations (3)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001236913.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Arg1198*) in the ELP1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in ELP1 are known to be pathogenic (PMID: 18303054, 24173031). This variant is present in population databases (rs376078668, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with ELP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 553107). For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024

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