VCV000000683.10 - ClinVar

NM_000147.5(FUCA1):c.1138G>T (p.Glu380Ter)

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(5)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

criteria provided, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_000147.5(FUCA1):c.1138G>T (p.Glu380Ter)

Variation ID: 683 Accession: VCV000000683.10

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 1p36.11 1: 23848671 (GRCh38) [ NCBI UCSC ] 1: 24175161 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Apr 4, 2013	Oct 26, 2024	Jan 14, 2024

HGVS

Nucleotide	Protein	Molecular consequence
NM_000147.5:c.1138G>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_000138.2:p.Glu380Ter	nonsense
NC_000001.11:g.23848671C>A
NC_000001.10:g.24175161C>A
NG_013346.1:g.24699G>T

Protein change

E380*

Other names

FUCA1, GLU375TER

Canonical SPDI

NC_000001.11:23848670:C:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

ClinGen: CA114436 OMIM: 612280.0003 dbSNP: rs80358195 VarSome

Comment on variant

NCBI staff reviewed the sequence information reported in PubMed 1281988 to determine the location of this allele on current reference sequence (E380*).

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
FUCA1		-	-	GRCh38 GRCh37	363	444

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Fucosidosis	Pathogenic (4)	criteria provided, multiple submitters, no conflicts	Jan 14, 2024	RCV000000718.11
not provided	Pathogenic (1)	criteria provided, single submitter	Mar 28, 2023	RCV003159089.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Aug 24, 2017)	criteria provided, single submitter (LabCorp Variant Classification Summary - May 2015) Method: clinical testing	Fucosidosis Affected status: unknown Allele origin: germline	Women's Health and Genetics/Laboratory Corporation of America, LabCorp Accession: SCV000695632.1 First in ClinVar: Oct 11, 2015 Last updated: Oct 11, 2015	Publications: PubMed (1) PubMed: 8504303 Comment: Variant summary: The FUCA1 c.1138G>T (p.Glu380X) variant results in a premature termination codon, predicted to cause a truncated or absent FUCA1 protein due to nonsense … (more) Variant summary: The FUCA1 c.1138G>T (p.Glu380X) variant results in a premature termination codon, predicted to cause a truncated or absent FUCA1 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. This variant was found in 1/121368 control chromosomes at a frequency of 0.0000082, which does not exceed the estimated maximal expected allele frequency of a pathogenic FUCA1 variant (0.001118). A publication, Seo_1993, cites the variant in eight Hispanic homozygous FUCO pts. In addition, a reputable database cites the variant as pathogenic. Taken together, this variant is classified as pathogenic. (less)
Pathogenic (Mar 28, 2023)	criteria provided, single submitter (GeneDx Variant Classification Process June 2021) Method: clinical testing	Not Provided Affected status: yes Allele origin: germline	GeneDx Accession: SCV003852911.1 First in ClinVar: Apr 09, 2023 Last updated: Apr 09, 2023	Comment: Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene … (more) Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 2803224, 1281988, 8739734, 8504303) (less)
Pathogenic (Jan 14, 2024)	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015)) Method: clinical testing	Fucosidosis Affected status: unknown Allele origin: germline	Labcorp Genetics (formerly Invitae), Labcorp Accession: SCV000752033.6 First in ClinVar: Oct 11, 2015 Last updated: Feb 20, 2024	Publications: PubMed (4) PubMed: 10094192‚ 1281988‚ 8504303‚ 8739734 Comment: This sequence change creates a premature translational stop signal (p.Glu380) in the FUCA1 gene. It is expected to result in an absent or disrupted protein … (more) This sequence change creates a premature translational stop signal (p.Glu380) 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). This variant is present in population databases (rs80358195, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with fucosidosis (PMID: 1281988, 8504303, 8739734). It is commonly reported in individuals of Hispanic-American ancestry (PMID: 1281988, 8504303, 8739734). This variant is also known as Glu375X. ClinVar contains an entry for this variant (Variation ID: 683). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects FUCA1 function (PMID: 1281988). For these reasons, this variant has been classified as Pathogenic. (less)
Pathogenic (Dec 15, 1992)	no assertion criteria provided Method: literature only	FUCOSIDOSIS Affected status: not provided Allele origin: germline	OMIM Accession: SCV000020868.1 First in ClinVar: Apr 04, 2013 Last updated: Apr 04, 2013	Publications: PubMed (1) PubMed: 1281988 Comment on evidence: In a patient with fucosidosis (230000), Yang et al. (1992) demonstrated a G-to-T transition at nucleotide 1141 changing glu375 (GAA) to a stop codon (UAA). … (more) In a patient with fucosidosis (230000), Yang et al. (1992) demonstrated a G-to-T transition at nucleotide 1141 changing glu375 (GAA) to a stop codon (UAA). The mother, referred to as 'the maternal parent,' was heterozygous. Though little information was given on the clinical picture, the disorder was presumably of the early-onset and severe type. (less)
Likely pathogenic (Jun 01, 2022)	no assertion criteria provided Method: provider interpretation	Fucosidosis Affected status: yes Allele origin: inherited	Solve-RD Consortium Accession: SCV005091543.1 First in ClinVar: Oct 26, 2024 Last updated: Oct 26, 2024 Comment: Variant identified during reanalysis of unsolved cases by the Solve-RD project. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and … (more) Variant identified during reanalysis of unsolved cases by the Solve-RD project. The Solve-RD project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 779257. (less)	Comment: Variant confirmed as disease-causing by referring clinical team

Comment:

Variant summary: The FUCA1 c.1138G>T (p.Glu380X) variant results in a premature termination codon, predicted to cause a truncated or absent FUCA1 protein due to nonsense mediated decay, which are commonly known mechanisms for disease. This variant was found in 1/121368 control chromosomes at a frequency of 0.0000082, which does not exceed the estimated maximal expected allele frequency of a pathogenic FUCA1 variant (0.001118). A publication, Seo_1993, cites the variant in eight Hispanic homozygous FUCO pts. In addition, a reputable database cites the variant as pathogenic. Taken together, this variant is classified as pathogenic.

Comment:

Not observed at significant frequency in large population cohorts (gnomAD); Nonsense variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 25525159, 2803224, 1281988, 8739734, 8504303)

Comment:

This sequence change creates a premature translational stop signal (p.Glu380*) 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). This variant is present in population databases (rs80358195, gnomAD 0.006%). This premature translational stop signal has been observed in individual(s) with fucosidosis (PMID: 1281988, 8504303, 8739734). It is commonly reported in individuals of Hispanic-American ancestry (PMID: 1281988, 8504303, 8739734). This variant is also known as Glu375X. ClinVar contains an entry for this variant (Variation ID: 683). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies have shown that this premature translational stop signal affects FUCA1 function (PMID: 1281988). For these reasons, this variant has been classified as Pathogenic.

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Comment:

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Spectrum of mutations in fucosidosis.	Willems PJ	European journal of human genetics : EJHG	1999	PMID: 10094192
Mutations in fucosidosis gene: a review.	Tiberio G	Acta geneticae medicae et gemellologiae	1995	PMID: 8739734
Fucosidosis: four new mutations and a new polymorphism.	Seo HC	Human molecular genetics	1993	PMID: 8504303
A mutation generating a stop codon in the alpha-L-fucosidase gene of a fucosidosis patient.	Yang M	Biochemical and biophysical research communications	1992	PMID: 1281988

Text-mined citations for rs80358195 ...

These citations are identified by LitVar using the rs number, so they may include citations for more than one variant at this location. Please review the LitVar results carefully for your variant of interest.

Record last updated Oct 27, 2024

ClinVar Genomic variation as it relates to human health

NM_000147.5(FUCA1):c.1138G>T (p.Glu380Ter)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs80358195 ...