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NM_000147.5(FUCA1):c.216G>A (p.Trp72Ter) AND Fucosidosis

Germline classification:
Likely pathogenic (1 submission)
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:
RCV003340936.2

Allele description [Variation Report for NM_000147.5(FUCA1):c.216G>A (p.Trp72Ter)]

NM_000147.5(FUCA1):c.216G>A (p.Trp72Ter)

Gene:
FUCA1:alpha-L-fucosidase 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
1p36.11
Genomic location:
Preferred name:
NM_000147.5(FUCA1):c.216G>A (p.Trp72Ter)
HGVS:
  • NC_000001.11:g.23868071C>T
  • NG_013346.1:g.5299G>A
  • NM_000147.5:c.216G>AMANE SELECT
  • NP_000138.2:p.Trp72Ter
  • NC_000001.10:g.24194561C>T
  • NR_174379.1:n.220G>A
  • NR_174380.1:n.220G>A
  • NR_174381.1:n.220G>A
  • NR_174382.1:n.220G>A
Protein change:
W72*
Molecular consequence:
  • NR_174379.1:n.220G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_174380.1:n.220G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_174381.1:n.220G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NR_174382.1:n.220G>A - non-coding transcript variant - [Sequence Ontology: SO:0001619]
  • NM_000147.5:c.216G>A - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:
Fucosidosis
Synonyms:
Alpha-l-fucosidase deficiency; Lysosomal storage disease caused by defective alpha-L-fucosidase with accumulation of fucose in the tissues
Identifiers:
MONDO: MONDO:0009254; MedGen: C0016788; Orphanet: 349; OMIM: 230000

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV004047807Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Likely pathogenicgermlineclinical 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, SCV004047807.1

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

Description

The stop gained variant c.216G>A (p.Trp72Ter) in FUCA1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.216G>A variant is reported with allele frequency 0.0004% in gnomAD exomes and novel in 1000 Genomes. The nucleotide change c.216G>A in FUCA1 is predicted as conserved by GERP++ and PhyloP across 100 vertebrates. This variant is predicted to cause loss of normal protein function. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely pathogenic . In the absence of another reportable variant , the molecular diagnosis is not confirmed

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

Last Updated: Apr 6, 2024