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NM_013245.3(VPS4A):c.944C>T (p.Thr315Met) AND Cerebellar hypoplasia-intellectual disability-congenital microcephaly-dystonia-anemia-growth retardation syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Mar 1, 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:
RCV003448832.2

Allele description [Variation Report for NM_013245.3(VPS4A):c.944C>T (p.Thr315Met)]

NM_013245.3(VPS4A):c.944C>T (p.Thr315Met)

Gene:
VPS4A:vacuolar protein sorting 4 homolog A [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
16q22.1
Genomic location:
Preferred name:
NM_013245.3(VPS4A):c.944C>T (p.Thr315Met)
HGVS:
  • NC_000016.10:g.69321143C>T
  • NM_013245.3:c.944C>TMANE SELECT
  • NP_037377.1:p.Thr315Met
  • NC_000016.9:g.69355046C>T
Protein change:
T315M
Molecular consequence:
  • NM_013245.3:c.944C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Cerebellar hypoplasia-intellectual disability-congenital microcephaly-dystonia-anemia-growth retardation syndrome
Synonyms:
CIMDAG SYNDROME; CEREBELLAR HYPOPLASIA, CATARACTS, IMPAIRED INTELLECTUAL DEVELOPMENT, CONGENITAL MICROCEPHALY, DYSTONIA, DYSERYTHROPOIETIC ANEMIA, AND GROWTH RETARDATION
Identifiers:
MONDO: MONDO:0035819; MedGen: C5543287; OMIM: 619273

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004176599Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Mar 1, 2023) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot 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 Neuberg Centre For Genomic Medicine, NCGM, SCV004176599.1

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

Description

The missense c.944C>T (p.Thr315Met)variant in VPS4A gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The p.Thr315Met variant has allele freuency 0.0005% in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. This variant has not been reported to the ClinVar database. The amino acid change p.Thr315Met in VPS4A is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. The amino acid Thr at position 315 is changed to a Met changing protein sequence and it might alter its composition and physico-chemical properties. For these reasons, this variant has been classified as Variant of Uncertain Significance (VUS).

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

Last Updated: Apr 6, 2024