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NM_000174.5(GP9):c.212T>C (p.Phe71Ser) AND not provided

Germline classification:
Pathogenic (1 submission)
Last evaluated:
Nov 21, 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:
RCV001204218.6

Allele description [Variation Report for NM_000174.5(GP9):c.212T>C (p.Phe71Ser)]

NM_000174.5(GP9):c.212T>C (p.Phe71Ser)

Gene:
GP9:glycoprotein IX platelet [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
3q21.3
Genomic location:
Preferred name:
NM_000174.5(GP9):c.212T>C (p.Phe71Ser)
Other names:
F55S
HGVS:
  • NC_000003.12:g.129061951T>C
  • NG_008715.1:g.6150T>C
  • NM_000174.5:c.212T>CMANE SELECT
  • NP_000165.1:p.Phe71Ser
  • NP_000165.1:p.Phe71Ser
  • LRG_477t1:c.212T>C
  • LRG_477:g.6150T>C
  • LRG_477p1:p.Phe71Ser
  • NC_000003.11:g.128780794T>C
  • NM_000174.3:c.212T>C
  • NM_000174.4:c.212T>C
  • P14770:p.Phe71Ser
Protein change:
F71S; PHE55SER
Links:
UniProtKB: P14770#VAR_024999; OMIM: 173515.0003; dbSNP: rs121918037
NCBI 1000 Genomes Browser:
rs121918037
Molecular consequence:
  • NM_000174.5:c.212T>C - missense variant - [Sequence Ontology: SO:0001583]

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
SCV001375417Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))		Pathogenic
(Nov 21, 2023) 		germlineclinical testing

PubMed (6)
[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

A phenylalanine-55 to serine amino-acid substitution in the human glycoprotein IX leucine-rich repeat is associated with Bernard-Soulier syndrome.

Noris P, Simsek S, Stibbe J, von dem Borne AE.

Br J Haematol. 1997 May;97(2):312-20.

PubMed [citation]
PMID:
9163595

Functional and molecular characterization of inherited platelet disorders in the Iberian Peninsula: results from a collaborative study.

Sánchez-Guiu I, Antón AI, Padilla J, Velasco F, Lucia JF, Lozano M, Cid AR, Sevivas T, Lopez-Fernandez MF, Vicente V, González-Manchón C, Rivera J, Lozano ML.

Orphanet J Rare Dis. 2014 Dec 24;9:213. doi: 10.1186/s13023-014-0213-6.

PubMed [citation]
PMID:
25539746
PMCID:
PMC4302577
See all PubMed Citations (6)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001375417.5

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (6)

Description

This sequence change replaces phenylalanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 71 of the GP9 protein (p.Phe71Ser). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individuals with Bernard-Soulier Syndrome and/or Bernard-Soulier syndrome (PMID: 9163595, 21699652, 25539746, 28395735, 29636940). This variant is also known as Phe55Ser. ClinVar contains an entry for this variant (Variation ID: 13531). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. This variant disrupts the p.Phe71 amino acid residue in GP9. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 21699652; Invitae). This suggests that this residue is clinically significant, and that variants that disrupt this residue 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