NM_003640.5(ELP1):c.3475dup (p.His1159fs) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Oct 23, 2021
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:: RCV001893299.3

Allele description [Variation Report for NM_003640.5(ELP1):c.3475dup (p.His1159fs)]

NM_003640.5(ELP1):c.3475dup (p.His1159fs)

Gene:

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

Variant type:

Duplication

Cytogenetic location:

9q31.3

Genomic location:

Preferred name:

NM_003640.5(ELP1):c.3475dup (p.His1159fs)

HGVS:

NC_000009.12:g.108879546dup
NG_008788.1:g.59786dup
NM_001318360.2:c.3133dup
NM_001330749.2:c.2428dup
NM_003640.5:c.3475dupMANE SELECT
NP_001305289.1:p.His1045fs
NP_001317678.1:p.His810fs
NP_003631.2:p.His1159fs
LRG_251:g.59786dup
NC_000009.11:g.111641822_111641823insG
NC_000009.11:g.111641826dup

Protein change:

H1045fs

Links:

dbSNP: rs2118938912

NCBI 1000 Genomes Browser:

rs2118938912

Molecular consequence:

NM_001318360.2:c.3133dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_001330749.2:c.2428dup - frameshift variant - [Sequence Ontology: SO:0001589]
NM_003640.5:c.3475dup - frameshift variant - [Sequence Ontology: SO:0001589]

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
SCV002165718	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Oct 23, 2021)	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

SCV002165718

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Oct 23, 2021)

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 Invitae, SCV002165718.3

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

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with ELP1-related conditions. This variant is not present in population databases (ExAC no frequency). This sequence change creates a premature translational stop signal (p.His1159Profs*10) 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).

#	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: Feb 20, 2024

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