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NM_000267.3(NF1):c.4168C>T (p.Leu1390Phe)

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Interpretation:
Pathogenic/Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
6 (Most recent: Feb 11, 2021)
Last evaluated:
Oct 26, 2020
Accession:
VCV000030992.5
Variation ID:
30992
Description:
single nucleotide variant
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NM_000267.3(NF1):c.4168C>T (p.Leu1390Phe)

Allele ID
39949
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
17q11.2
Genomic location
17: 31258401 (GRCh38) GRCh38 UCSC
17: 29585419 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000017.10:g.29585419C>T
NC_000017.11:g.31258401C>T
NM_000267.3:c.4168C>T NP_000258.1:p.Leu1390Phe missense
... more HGVS
Protein change
L1390F, L1411F
Other names
-
Canonical SPDI
NC_000017.11:31258400:C:T
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA129599
UniProtKB/Swiss-Prot: VAR_065236
OMIM: 613113.0045
dbSNP: rs199474789
Varsome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Pathogenic/Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Oct 26, 2020 RCV000195735.8
Likely pathogenic 2 criteria provided, single submitter Nov 29, 2016 RCV000059194.1
Pathogenic 1 no assertion criteria provided Dec 1, 2009 RCV000023983.5
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
NF1 Sufficient evidence for dosage pathogenicity No evidence available GRCh38
GRCh37
7722 7932

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter Supporting information
Pathogenic
(Dec 20, 2018)
criteria provided, single submitter
Method: clinical testing
Neurofibromatosis, type 1
(Autosomal dominant inheritance)
Allele origin: germline
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital
Accession: SCV000863575.1
Submitted: (Dec 20, 2018)
Evidence details
Likely pathogenic
(Oct 26, 2020)
criteria provided, single submitter
Method: clinical testing
Neurofibromatosis, type 1
Allele origin: germline
Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV001478945.1
Submitted: (Feb 11, 2021)
Evidence details
Likely pathogenic
(Nov 29, 2016)
criteria provided, single submitter
Method: clinical testing
Not Provided
Allele origin: germline
GeneDx
Accession: SCV000491217.3
Submitted: (Jan 29, 2019)
Evidence details
Comment:
The L1390F variant has been observed previously in one family with neurofibromatosis-Noonan syndrome (NFNS) (Nyström et al., 2009). The variant was not observed in approximately … (more)
Pathogenic
(Feb 26, 2020)
criteria provided, single submitter
Method: clinical testing
Neurofibromatosis, type 1
Allele origin: germline
Invitae
Accession: SCV000253693.7
Submitted: (Jan 07, 2021)
Evidence details
Publications
PubMed (2)
Comment:
This sequence change replaces leucine with phenylalanine at codon 1390 of the NF1 protein (p.Leu1390Phe). The leucine residue is highly conserved and there is a … (more)
Pathogenic
(Dec 01, 2009)
no assertion criteria provided
Method: literature only
NEUROFIBROMATOSIS-NOONAN SYNDROME
Allele origin: germline
OMIM
Accession: SCV000045274.4
Submitted: (Mar 16, 2012)
Evidence details
Publications
PubMed (2)
not provided
(-)
no assertion provided
Method: not provided
not provided
Allele origin: not provided
UniProtKB/Swiss-Prot
Accession: SCV000090723.1
Submitted: (Mar 26, 2012)
Evidence details

Functional evidence

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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.

Citations for this variant

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Title Author Journal Year Link
Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. Nykamp K Genetics in medicine : official journal of the American College of Medical Genetics 2017 PMID: 28492532
Noonan syndrome and neurofibromatosis type I in a family with a novel mutation in NF1. Nyström AM Clinical genetics 2009 PMID: 19845691
Noonan syndrome with café-au-lait spots and multiple lentigines syndrome are not linked to the neurofibromatosis type 1 locus. Ahlbom BE Clinical genetics 1995 PMID: 7586657

Text-mined citations for rs199474789...

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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 May 10, 2021