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NM_001042492.3(NF1):c.2968A>C (p.Thr990Pro) AND Hereditary cancer-predisposing syndrome

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 7, 2015
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:
RCV000219343.1

Allele description [Variation Report for NM_001042492.3(NF1):c.2968A>C (p.Thr990Pro)]

NM_001042492.3(NF1):c.2968A>C (p.Thr990Pro)

Gene:
NF1:neurofibromin 1 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
17q11.2
Genomic location:
Preferred name:
NM_001042492.3(NF1):c.2968A>C (p.Thr990Pro)
HGVS:
  • NC_000017.11:g.31229952A>C
  • NG_009018.1:g.139976A>C
  • NM_000267.3:c.2968A>C
  • NM_001042492.3:c.2968A>CMANE SELECT
  • NP_000258.1:p.Thr990Pro
  • NP_001035957.1:p.Thr990Pro
  • NP_001035957.1:p.Thr990Pro
  • LRG_214t1:c.2968A>C
  • LRG_214t2:c.2968A>C
  • LRG_214:g.139976A>C
  • LRG_214p1:p.Thr990Pro
  • LRG_214p2:p.Thr990Pro
  • NC_000017.10:g.29556970A>C
  • NM_001042492.2:c.2968A>C
  • NM_001042492.3:c.2968A>C
Protein change:
T990P
Links:
dbSNP: rs876658299
NCBI 1000 Genomes Browser:
rs876658299
Molecular consequence:
  • NM_000267.3:c.2968A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001042492.3:c.2968A>C - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Name:
Hereditary cancer-predisposing syndrome
Synonyms:
Neoplastic Syndromes, Hereditary; Tumor predisposition; Cancer predisposition; See all synonyms [MedGen]
Identifiers:
MONDO: MONDO:0015356; MeSH: D009386; MedGen: C0027672

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000273339Ambry Genetics
criteria provided, single submitter

(Ambry Autosomal Dominant and X-Linked criteria (10/2015))		Uncertain significance
(Jan 7, 2015) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknown1not providednot provided1not providedclinical testing

Details of each submission

From Ambry Genetics, SCV000273339.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

The p.T990P variant (also known as c.2968A>C), located in coding exon 22 of the NF1 gene, results from an A to C substitution at nucleotide position 2968. The threonine at codon 990 is replaced by proline, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6500 samples (13000 alleles) with coverage at this position. To date, this alteration has been detected with an allele frequency of approximately 0.003% (greater than 30000 alleles tested) in our clinical cohort. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of p.T990P remains unclear.

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknown1not providednot provided1not providednot providednot provided

Last Updated: Feb 14, 2024