NM_000147.5(FUCA1):c.1131_1132delinsTT (p.Gln378Ter) AND Fucosidosis

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Jun 11, 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:: RCV003496416.2

Allele description [Variation Report for NM_000147.5(FUCA1):c.1131_1132delinsTT (p.Gln378Ter)]

NM_000147.5(FUCA1):c.1131_1132delinsTT (p.Gln378Ter)

Gene:

FUCA1:alpha-L-fucosidase 1 [Gene - OMIM - HGNC]

Variant type:

Indel

Cytogenetic location:

1p36.11

Genomic location:

Preferred name:

NM_000147.5(FUCA1):c.1131_1132delinsTT (p.Gln378Ter)

HGVS:

NC_000001.11:g.23848677_23848678delinsAA
NG_013346.1:g.24692_24693delinsTT
NM_000147.5:c.1131_1132delinsTTMANE SELECT
NP_000138.2:p.Gln378Ter
NC_000001.10:g.24175167_24175168delinsAA
NR_174379.1:n.1309_1310delinsTT
NR_174380.1:n.1358_1359delinsTT
NR_174381.1:n.1197_1198delinsTT
NR_174382.1:n.1594_1595delinsTT

Protein change:

Q378*

Molecular consequence:

NR_174379.1:n.1309_1310delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_174380.1:n.1358_1359delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_174381.1:n.1197_1198delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NR_174382.1:n.1594_1595delinsTT - non-coding transcript variant - [Sequence Ontology: SO:0001619]
NM_000147.5:c.1131_1132delinsTT - 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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004265835	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jun 11, 2023)	germline	clinical testing	PubMed (2) [See all records that cite these PMIDs] 10094192, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004265835

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jun 11, 2023)

germline

clinical testing

PubMed (2)
[See all records that cite these PMIDs]

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

Spectrum of mutations in fucosidosis.

Willems PJ, Seo HC, Coucke P, Tonlorenzi R, O'Brien JS.

Eur J Hum Genet. 1999 Jan;7(1):60-7. Review.

PubMed [citation]

PMID:: 10094192

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, SCV004265835.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (2)

Description

For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with FUCA1-related conditions. Information on the frequency of this variant in the gnomAD database is not available, as this variant may be reported differently in the database. This sequence change creates a premature translational stop signal (p.Gln378*) in the FUCA1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in FUCA1 are known to be pathogenic (PMID: 10094192).

#	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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