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NM_003640.5(ELP1):c.3259G>A (p.Ala1087Thr) AND Medulloblastoma

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Nov 11, 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:
RCV001789773.3

Allele description [Variation Report for NM_003640.5(ELP1):c.3259G>A (p.Ala1087Thr)]

NM_003640.5(ELP1):c.3259G>A (p.Ala1087Thr)

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.3259G>A (p.Ala1087Thr)
HGVS:
  • NC_000009.12:g.108882151C>T
  • NG_008788.1:g.57178G>A
  • NM_001318360.2:c.2917G>A
  • NM_001330749.2:c.2212G>A
  • NM_003640.5:c.3259G>AMANE SELECT
  • NP_001305289.1:p.Ala973Thr
  • NP_001317678.1:p.Ala738Thr
  • NP_003631.2:p.Ala1087Thr
  • LRG_251t1:c.3259G>A
  • LRG_251:g.57178G>A
  • NC_000009.11:g.111644431C>T
  • NM_003640.3:c.3259G>A
  • NM_003640.4:c.3259G>A
Protein change:
A1087T
Links:
dbSNP: rs61749203
NCBI 1000 Genomes Browser:
rs61749203
Molecular consequence:
  • NM_001318360.2:c.2917G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001330749.2:c.2212G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003640.5:c.3259G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Medulloblastoma (MDB)
Synonyms:
Medulloblastoma, somatic; MEDULLOBLASTOMA PREDISPOSITION SYNDROME
Identifiers:
MONDO: MONDO:0007959; MeSH: D008527; MedGen: C0025149; Orphanet: 616; OMIM: 155255; Human Phenotype Ontology: HP:0002885

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002032282St. Jude Molecular Pathology, St. Jude Children's Research Hospital
criteria provided, single submitter

(St. Jude Assertion Criteria 2020)		Uncertain significance
(Nov 11, 2021) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From St. Jude Molecular Pathology, St. Jude Children's Research Hospital, SCV002032282.2

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

Description

The ELP1 c.3259G>A (p.Ala1087Thr) missense change has a maximum subpopulation frequency of 0.0097% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/variant/9-111644431-C-T?dataset=gnomad_r2_1). Five of seven in silico tools predict a benign effect of this variant on protein function (BP4), but to our knowledge these predictions have not been confirmed by functional assays. To our knowledge, this variant has not been reported in individuals with a personal or family history of medulloblastoma. In summary, this variant meets criteria to be classified as of uncertain significance based on the ACMG/AMP criteria: BP4

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

Last Updated: May 16, 2025