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NM_007198.4(PLPBP):c.207+1G>C AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Dec 28, 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:
RCV003026904.2

Allele description [Variation Report for NM_007198.4(PLPBP):c.207+1G>C]

NM_007198.4(PLPBP):c.207+1G>C

Gene:
PLPBP:pyridoxal phosphate binding protein [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
8p11.23
Genomic location:
Preferred name:
NM_007198.4(PLPBP):c.207+1G>C
HGVS:
  • NC_000008.11:g.37765634G>C
  • NG_053030.1:g.8882G>C
  • NM_001349346.2:c.207+1G>C
  • NM_001349347.2:c.207+1G>C
  • NM_001349348.2:c.51+1G>C
  • NM_001349349.1:c.312+1G>C
  • NM_007198.4:c.207+1G>CMANE SELECT
  • NC_000008.10:g.37623152G>C
Molecular consequence:
  • NM_001349346.2:c.207+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001349347.2:c.207+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001349348.2:c.51+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_001349349.1:c.312+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]
  • NM_007198.4:c.207+1G>C - splice donor variant - [Sequence Ontology: SO:0001575]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003328406Invitae
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Dec 28, 2023) 		germlineclinical testing

PubMed (4)
[See all records that cite these PMIDs]

Help

Summary from all submissions

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

Citations

PubMed

Splicing in action: assessing disease causing sequence changes.

Baralle D, Baralle M.

J Med Genet. 2005 Oct;42(10):737-48. Review.

PubMed [citation]
PMID:
16199547
PMCID:
PMC1735933

Mutations in PROSC Disrupt Cellular Pyridoxal Phosphate Homeostasis and Cause Vitamin-B(6)-Dependent Epilepsy.

Darin N, Reid E, Prunetti L, Samuelsson L, Husain RA, Wilson M, El Yacoubi B, Footitt E, Chong WK, Wilson LC, Prunty H, Pope S, Heales S, Lascelles K, Champion M, Wassmer E, Veggiotti P, de Crécy-Lagard V, Mills PB, Clayton PT.

Am J Hum Genet. 2016 Dec 1;99(6):1325-1337. doi: 10.1016/j.ajhg.2016.10.011.

PubMed [citation]
PMID:
27912044
PMCID:
PMC5142116
See all PubMed Citations (4)

Details of each submission

From Invitae, SCV003328406.2

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

This sequence change affects a donor splice site in intron 2 of the PROSC gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PROSC are known to be pathogenic (PMID: 27912044). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individual(s) with pyridoxine-dependent epilepsy (PMID: 27912044, 31741821). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 2112606). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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: Feb 28, 2024