NM_000147.5(FUCA1):c.1123T>C (p.Trp375Arg) AND Fucosidosis

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 7, 2022
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:: RCV003007295.2

Allele description [Variation Report for NM_000147.5(FUCA1):c.1123T>C (p.Trp375Arg)]

NM_000147.5(FUCA1):c.1123T>C (p.Trp375Arg)

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.1123T>C (p.Trp375Arg)

HGVS:

NC_000001.11:g.23848686A>G
NG_013346.1:g.24684T>C
NM_000147.5:c.1123T>CMANE SELECT
NP_000138.2:p.Trp375Arg
NC_000001.10:g.24175176A>G
NR_174379.1:n.1301T>C
NR_174380.1:n.1350T>C
NR_174381.1:n.1189T>C
NR_174382.1:n.1586T>C

Protein change:

W375R

Molecular consequence:

NM_000147.5:c.1123T>C - missense variant - [Sequence Ontology: SO:0001583]
NR_174379.1:n.1301T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_174380.1:n.1350T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_174381.1:n.1189T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_174382.1:n.1586T>C - non-coding transcript variant - [Sequence Ontology: SO:0001619]

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

Recent activity

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95488[uid] (1)
Taxonomy
Mus musculus targeted KO-first, conditional ready, lacZ-tagged mutant allele Sv2...
Mus musculus targeted KO-first, conditional ready, lacZ-tagged mutant allele Sv2a:tm1a(EUCOMM)Hmgu; transgenic
gi|354793796|gb|JN958297.1|

Nucleotide
Chromosome neighbors for GEO Profiles (Select 9080971) (20)
GEO Profiles
Nucleotide Links for Gene (Select 855309) (3)
Nucleotide
Leptolobium brachystachyum voucher R.Schutz-Rodrigues 1293 (UEC) tRNA-Leu (trnL)...
Leptolobium brachystachyum voucher R.Schutz-Rodrigues 1293 (UEC) tRNA-Leu (trnL) gene, intron; chloroplast
gi|400532132|gb|JX124447.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV003297277	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 7, 2022)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV003297277

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 7, 2022)

germline

clinical testing

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

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

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV003297277.1

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

Description

This sequence change replaces tryptophan, which is neutral and slightly polar, with arginine, which is basic and polar, at codon 375 of the FUCA1 protein (p.Trp375Arg). This variant is present in population databases (no rsID available, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with FUCA1-related conditions. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.

#	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: Sep 29, 2024

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