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NM_032793.5(MFSD2A):c.228+8G>A AND Microcephaly 15, primary, autosomal recessive

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 28, 2019
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:
RCV002470519.1

Allele description [Variation Report for NM_032793.5(MFSD2A):c.228+8G>A]

NM_032793.5(MFSD2A):c.228+8G>A

Gene:
MFSD2A:MFSD2 lysolipid transporter A, lysophospholipid [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p34.2
Genomic location:
Preferred name:
NM_032793.5(MFSD2A):c.228+8G>A
HGVS:
  • NC_000001.11:g.39957229G>A
  • NG_053084.1:g.7118G>A
  • NM_001136493.3:c.228+8G>A
  • NM_001287808.2:c.-116+1844G>A
  • NM_001287809.2:c.117+8G>A
  • NM_001349821.2:c.222+8G>A
  • NM_001349822.2:c.228+8G>A
  • NM_001349823.2:c.-118+8G>A
  • NM_032793.5:c.228+8G>AMANE SELECT
  • NC_000001.10:g.40422901G>A
  • NM_032793.4:c.228+8G>A
Molecular consequence:
  • NM_001136493.3:c.228+8G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001287808.2:c.-116+1844G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001287809.2:c.117+8G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349821.2:c.222+8G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349822.2:c.228+8G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001349823.2:c.-118+8G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_032793.5:c.228+8G>A - intron variant - [Sequence Ontology: SO:0001627]

Condition(s)

Name:
Microcephaly 15, primary, autosomal recessive (NEDMISBA)
Synonyms:
NEURODEVELOPMENTAL DISORDER WITH PROGRESSIVE MICROCEPHALY, SPASTICITY, AND BRAIN IMAGING ABNORMALITIES
Identifiers:
MONDO: MONDO:0014660; MedGen: C4225310; Orphanet: 2512; OMIM: 616486

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002768659Victorian Clinical Genetics Services, Murdoch Childrens Research Institute

See additional submitters

criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significance
(Aug 28, 2019) 		germlineclinical testing

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

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot 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 Victorian Clinical Genetics Services, Murdoch Childrens Research Institute, SCV002768659.1

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

Description

A heterozygous splice-site variant, NM_032793.4(MFSD2A):c.228+8G>A, has been identified in intron 2 of 13 of the MFSD2A gene. The effect of this variant on the protein sequence is unknown. The nucleotide at this position has low conservation (Phylop UCSC). This nucleotide substitution is predicted to generate a new donor site (HSF) but is not predicted to cause aberrant splicing of exon in in the MFSD2A gene (FruitFly, NetGene2); further testing via RNA studies are required to confirm if splicing is altered. The variant is present in the gnomAD database at a frequency of 0.0009% (2 heterozygotes, 0 homozygotes) but has not been previously reported in clinical cases. Based on the information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS) with LOW CLINICAL RELEVANCE.

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

Last Updated: Aug 5, 2023