ClinVar Genomic variation as it relates to human health
NM_001042492.3(NF1):c.1994C>T (p.Ser665Phe)
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Uncertain significance(1); Benign(15); Likely benign(6)
No data submitted for somatic clinical impact
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001042492.3(NF1):c.1994C>T (p.Ser665Phe)
Variation ID: 134881 Accession: VCV000134881.44
- Type and length
-
single nucleotide variant, 1 bp
- Location
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Cytogenetic: 17q11.2 17: 31225243 (GRCh38) [ NCBI UCSC ] 17: 29552261 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Jun 9, 2014 Oct 20, 2024 Aug 1, 2024 - HGVS
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Nucleotide Protein Molecular
consequenceNM_001042492.3:c.1994C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001035957.1:p.Ser665Phe missense NM_000267.3:c.1994C>T NP_000258.1:p.Ser665Phe missense NC_000017.11:g.31225243C>T NC_000017.10:g.29552261C>T NG_009018.1:g.135267C>T LRG_214:g.135267C>T LRG_214t1:c.1994C>T LRG_214p1:p.Ser665Phe LRG_214t2:c.1994C>T LRG_214p2:p.Ser665Phe P21359:p.Ser665Phe - Protein change
- S665F
- Other names
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NM_000267.3(NF1):c.1994C>T(p.Ser665Phe)
NM_001042492.2(NF1):c.1994C>T(p.Ser665Phe)
- Canonical SPDI
- NC_000017.11:31225242:C:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
- -
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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0.00140 (T)
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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Trans-Omics for Precision Medicine (TOPMed) 0.00217
The Genome Aggregation Database (gnomAD) 0.00220
NHLBI Exome Sequencing Project (ESP) Exome Variant Server 0.00231
The Genome Aggregation Database (gnomAD), exomes 0.00060
Exome Aggregation Consortium (ExAC) 0.00074
1000 Genomes Project 30x 0.00125
1000 Genomes Project 0.00140
- Links
Genes
Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
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HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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NF1 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh38 GRCh37 |
14135 | 14574 |
Conditions - Germline
Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
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Benign/Likely benign (5) |
criteria provided, multiple submitters, no conflicts
|
Feb 3, 2020 | RCV000121628.23 | |
Benign/Likely benign (3) |
criteria provided, multiple submitters, no conflicts
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Nov 15, 2022 | RCV000129662.5 | |
Conflicting interpretations of pathogenicity (7) |
criteria provided, conflicting classifications
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Feb 1, 2024 | RCV000200171.27 | |
Benign (3) |
criteria provided, multiple submitters, no conflicts
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Aug 1, 2024 | RCV000587577.17 | |
Benign (1) |
criteria provided, single submitter
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Nov 20, 2017 | RCV001124836.5 | |
Benign (2) |
criteria provided, multiple submitters, no conflicts
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Jul 7, 2023 | RCV001124835.6 | |
Benign (1) |
criteria provided, single submitter
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Nov 20, 2017 | RCV001124837.5 | |
Likely benign (1) |
criteria provided, single submitter
|
Apr 26, 2019 | RCV004558311.1 |
Submissions - Germline
Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Likely benign
(Nov 01, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
Neurofibromatosis, type 1
Affected status: yes
Allele origin:
germline
|
Center for Human Genetics, Inc, Center for Human Genetics, Inc
Accession: SCV000781933.1
First in ClinVar: May 26, 2018 Last updated: May 26, 2018 |
|
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Benign
(May 11, 2016)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
PreventionGenetics, part of Exact Sciences
Accession: SCV000806260.1
First in ClinVar: Sep 13, 2018 Last updated: Sep 13, 2018 |
|
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Benign
(Apr 07, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: not provided
Allele origin:
germline
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Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine
Accession: SCV000269447.3
First in ClinVar: May 29, 2016 Last updated: Sep 21, 2018 |
Comment:
p.Ser665Phe in exon 17 of NF1: This variant is not expected to have clinical sig nificance because it has been identified in 0.8% (81/10324) of … (more)
p.Ser665Phe in exon 17 of NF1: This variant is not expected to have clinical sig nificance because it has been identified in 0.8% (81/10324) of African chromosom es by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; db SNP rs145891889). (less)
Number of individuals with the variant: 5
|
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Benign
(Jan 30, 2019)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: unknown
Allele origin:
germline
|
Women's Health and Genetics/Laboratory Corporation of America, LabCorp
Accession: SCV000696388.2
First in ClinVar: Mar 17, 2018 Last updated: Nov 08, 2019 |
Comment:
Variant summary: NF1 c.1994C>T (p.Ser665Phe) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign … (more)
Variant summary: NF1 c.1994C>T (p.Ser665Phe) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00074 in 282364 control chromosomes, predominantly within the African subpopulation at a frequency of 0.0077 in the gnomAD database, including 2 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 37-fold of the estimated maximal expected allele frequency for a pathogenic variant in NF1 causing Neurofibromatosis Type 1 phenotype (0.00021), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. However, this region is affected by pseudogene interference therefore these population frequency data need to be cautiously considered. c.1994C>T has been reported in the literature in an affected individual (Fahsold 2000). This report however does not provide unequivocal conclusions about association of the variant with Neurofibromatosis Type 1. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Eight ClinVar submissions from other clinical diagnostic laboratories (evaluation after 2014) cite the variant predominantly as likely benign/benign (7x) and once as uncertain significance. Based on the evidence outlined above, the variant was classified as benign. (less)
|
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Likely benign
(Oct 26, 2020)
|
criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
Affected status: yes
Allele origin:
germline
|
Genome Diagnostics Laboratory, The Hospital for Sick Children
Accession: SCV001479096.1
First in ClinVar: Feb 13, 2021 Last updated: Feb 13, 2021 |
|
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Benign
(Aug 17, 2022)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, type 1
(Autosomal dominant inheritance)
Affected status: yes
Allele origin:
germline
|
Medical Genetics, University of Parma
Accession: SCV002567760.1
First in ClinVar: Aug 29, 2022 Last updated: Aug 29, 2022 |
|
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Benign
(Jul 07, 2023)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, familial spinal
Affected status: yes
Allele origin:
germline
|
KCCC/NGS Laboratory, Kuwait Cancer Control Center
Accession: SCV004016428.1
First in ClinVar: Jul 29, 2023 Last updated: Jul 29, 2023 |
|
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Benign
(Apr 28, 2017)
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criteria provided, single submitter
Method: clinical testing
|
not provided
Affected status: unknown
Allele origin:
unknown
|
Quest Diagnostics Nichols Institute San Juan Capistrano
Accession: SCV002774039.2
First in ClinVar: Dec 31, 2022 Last updated: Jan 06, 2024 |
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Likely benign
(Apr 26, 2019)
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criteria provided, single submitter
Method: clinical testing
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Cardiovascular phenotype
Hereditary cancer-predisposing syndrome
Explanation for multiple conditions: Uncertain.
The variant was classified for several related diseases, possibly a spectrum of disease; the variant may be associated with one or more the diseases.
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV005048590.1
First in ClinVar: Jun 09, 2024 Last updated: Jun 09, 2024 |
Comment:
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of … (more)
This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. (less)
|
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Benign
(Aug 01, 2024)
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criteria provided, single submitter
Method: clinical testing
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not provided
Affected status: yes
Allele origin:
germline
|
CeGaT Center for Human Genetics Tuebingen
Accession: SCV004184665.9
First in ClinVar: Dec 24, 2023 Last updated: Oct 20, 2024 |
Comment:
NF1: BS1, BS2
Number of individuals with the variant: 2
|
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Uncertain significance
(May 31, 2018)
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criteria provided, single submitter
Method: curation
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Neurofibromatosis, type 1
Affected status: unknown
Allele origin:
unknown
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SIB Swiss Institute of Bioinformatics
Accession: SCV000803613.1
First in ClinVar: May 26, 2018 Last updated: May 26, 2018 |
Comment:
This variant is interpreted as a Uncertain Significance - Insufficient Evidence, for Neurofibromatosis 1, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: BS1 … (more)
This variant is interpreted as a Uncertain Significance - Insufficient Evidence, for Neurofibromatosis 1, in Autosomal Dominant manner. The following ACMG Tag(s) were applied: BS1 => Allele frequency is greater than expected for disorder. (less)
|
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Benign
(Nov 20, 2017)
|
criteria provided, single submitter
Method: clinical testing
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Café-au-lait macules with pulmonary stenosis
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001283833.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
|
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Benign
(Nov 20, 2017)
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criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis, familial spinal
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001283831.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
|
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Benign
(Nov 20, 2017)
|
criteria provided, single submitter
Method: clinical testing
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Neurofibromatosis-Noonan syndrome
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001283832.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign. (less)
|
|
Benign
(Nov 20, 2017)
|
criteria provided, single submitter
Method: clinical testing
|
Neurofibromatosis, type 1
Affected status: unknown
Allele origin:
germline
|
Illumina Laboratory Services, Illumina
Accession: SCV001283834.1
First in ClinVar: May 31, 2020 Last updated: May 31, 2020 |
Comment:
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, … (more)
This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign. (less)
|
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Likely benign
(Sep 09, 2015)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Ambry Genetics
Accession: SCV000184460.5
First in ClinVar: Aug 06, 2014 Last updated: Sep 24, 2016 |
Comment:
In silico models in agreement (benign);Other data supporting benign classification;Subpopulation frequency in support of benign classification
Number of individuals with the variant: 1
|
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Benign
(May 05, 2021)
|
criteria provided, single submitter
Method: clinical testing
|
Not Provided
Affected status: yes
Allele origin:
germline
|
GeneDx
Accession: SCV000521058.5
First in ClinVar: Mar 08, 2017 Last updated: Sep 21, 2018 |
Comment:
This variant is associated with the following publications: (PMID: 10712197, 24803665, 15060124, 24728327, 27322474, 23771920, 28371134, 26154128, 33562071)
|
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Likely benign
(Feb 03, 2020)
|
criteria provided, single submitter
Method: clinical testing
|
not specified
Affected status: no
Allele origin:
germline
|
Genetic Services Laboratory, University of Chicago
Accession: SCV002066473.1
First in ClinVar: Jan 29, 2022 Last updated: Jan 29, 2022 |
|
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Benign
(Jul 31, 2020)
|
criteria provided, single submitter
Method: curation
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Sema4, Sema4
Accession: SCV002527436.1
First in ClinVar: Jun 24, 2022 Last updated: Jun 24, 2022 |
|
|
Likely benign
(Jul 02, 2018)
|
criteria provided, single submitter
Method: clinical testing
|
Neurofibromatosis, type 1
Affected status: unknown
Allele origin:
unknown
|
Mendelics
Accession: SCV000839134.2
First in ClinVar: Oct 10, 2018 Last updated: Dec 11, 2022 |
|
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Benign
(Nov 15, 2022)
|
criteria provided, single submitter
Method: clinical testing
|
Hereditary cancer-predisposing syndrome
Affected status: unknown
Allele origin:
germline
|
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.
Accession: SCV002819225.1
First in ClinVar: Jan 15, 2023 Last updated: Jan 15, 2023 |
|
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Benign
(Feb 01, 2024)
|
criteria provided, single submitter
Method: clinical testing
|
Neurofibromatosis, type 1
Affected status: unknown
Allele origin:
germline
|
Labcorp Genetics (formerly Invitae), Labcorp
Accession: SCV000252676.11
First in ClinVar: Oct 11, 2015 Last updated: Feb 20, 2024 |
|
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not provided
(Sep 19, 2013)
|
no classification provided
Method: reference population
|
AllHighlyPenetrant
Affected status: unknown
Allele origin:
germline
|
ITMI
Accession: SCV000085826.1
First in ClinVar: Jun 09, 2014 Last updated: Jun 09, 2014
Comment:
Please see associated publication for description of ethnicities
|
Observation 1:
Ethnicity/Population group: Whole_cohort
Observation 2:
Ethnicity/Population group: African
Observation 3:
Ethnicity/Population group: African_European
Observation 4:
Ethnicity/Population group: Central_Asian
Observation 5:
Ethnicity/Population group: East_Asian
Observation 6:
Ethnicity/Population group: European
Observation 7:
Ethnicity/Population group: Hispanic
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Germline Functional Evidence
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 germline classification of this variant
HelpTitle | Author | Journal | Year | Link |
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Novel Mutations in a Lethal Case of Lymphomatous Adult T Cell Lymphoma with Cryptic Myocardial Involvement. | Hashemi Zonouz T | Current oncology (Toronto, Ont.) | 2021 | PMID: 33562071 |
Comprehensive RNA Analysis of the NF1 Gene in Classically Affected NF1 Affected Individuals Meeting NIH Criteria has High Sensitivity and Mutation Negative Testing is Reassuring in Isolated Cases With Pigmentary Features Only. | Evans DG | EBioMedicine | 2016 | PMID: 27322474 |
Structure-energy-based predictions and network modelling of RASopathy and cancer missense mutations. | Kiel C | Molecular systems biology | 2014 | PMID: 24803665 |
Germline variation in cancer-susceptibility genes in a healthy, ancestrally diverse cohort: implications for individual genome sequencing. | Bodian DL | PloS one | 2014 | PMID: 24728327 |
Automated comparative sequence analysis identifies mutations in 89% of NF1 patients and confirms a mutation cluster in exons 11-17 distinct from the GAP related domain. | Mattocks C | Journal of medical genetics | 2004 | PMID: 15060124 |
Minor lesion mutational spectrum of the entire NF1 gene does not explain its high mutability but points to a functional domain upstream of the GAP-related domain. | Fahsold R | American journal of human genetics | 2000 | PMID: 10712197 |
Text-mined citations for rs145891889 ...
HelpRecord last updated Oct 20, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.