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NM_000507.4(FBP1):c.966del (p.Asp323fs) AND Fructose-biphosphatase deficiency

Germline classification:
Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:
Jan 16, 2024
Review status:
criteria provided, conflicting classifications
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:
RCV000661978.6

Allele description [Variation Report for NM_000507.4(FBP1):c.966del (p.Asp323fs)]

NM_000507.4(FBP1):c.966del (p.Asp323fs)

Gene:
FBP1:fructose-bisphosphatase 1 [Gene - OMIM - HGNC]
Variant type:
Deletion
Cytogenetic location:
9q22.32
Genomic location:
Preferred name:
NM_000507.4(FBP1):c.966del (p.Asp323fs)
HGVS:
  • NC_000009.12:g.94603436del
  • NG_008174.1:g.41818del
  • NM_000507.4:c.966delMANE SELECT
  • NM_001127628.2:c.966del
  • NP_000498.2:p.Asp323fs
  • NP_001121100.1:p.Asp323fs
  • NC_000009.11:g.97365714del
  • NC_000009.11:g.97365718del
  • NM_001127628.1:c.966delC
Protein change:
D323fs
Links:
dbSNP: rs747269745
NCBI 1000 Genomes Browser:
rs747269745
Molecular consequence:
  • NM_000507.4:c.966del - frameshift variant - [Sequence Ontology: SO:0001589]
  • NM_001127628.2:c.966del - frameshift variant - [Sequence Ontology: SO:0001589]
Observations:
1

Condition(s)

Name:
Fructose-biphosphatase deficiency (FBP1D)
Synonyms:
Baker-Winegrad disease; Fructose-1,6-Diphosphatase Deficiency; Fructose 1,6 Bisphosphatase Deficiency
Identifiers:
MONDO: MONDO:0009251; MedGen: C0016756; Orphanet: 348; OMIM: 229700

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000784309Genomic Research Center, Shahid Beheshti University of Medical Sciences
criteria provided, single submitter

(ACMG Guidelines, 2015)
Uncertain significance
(Mar 5, 2018)
inheritedclinical testing

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

SCV004294335Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jan 16, 2024)
germlineclinical testing

PubMed (3)
[See all records that cite these PMIDs]

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providedinheritedno1not 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

Novel mutations in patients with fructose-1,6-bisphosphatase deficiency.

Herzog B, Wendel U, Morris AA, Eschrich K.

J Inherit Metab Dis. 1999 Apr;22(2):132-8.

PubMed [citation]
PMID:
10234608
See all PubMed Citations (4)

Details of each submission

From Genomic Research Center, Shahid Beheshti University of Medical Sciences, SCV000784309.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testing PubMed (1)
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1inheritednonot providednot providednot provided1not providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004294335.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (3)

Description

This sequence change creates a premature translational stop signal (p.Asp323Thrfs*7) in the FBP1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 16 amino acid(s) of the FBP1 protein. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This premature translational stop signal has been observed in individual(s) with fructose-1,6-bisphosphatase deficiency (PMID: 10234608). ClinVar contains an entry for this variant (Variation ID: 548499). 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 FBP1 function (PMID: 10234608). This variant disrupts a region of the FBP1 protein in which other variant(s) (p.Leu329Pro) have been determined to be pathogenic (PMID: 30858132). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.

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

Last Updated: Sep 29, 2024