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NM_000310.4(PPT1):c.249CTT[2] (p.Phe85del)

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, multiple submitters, no conflicts
Submissions:
3 (Most recent: Mar 28, 2019)
Last evaluated:
Jan 4, 2019
Accession:
VCV000056185.2
Variation ID:
56185
Description:
3bp microsatellite
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NM_000310.4(PPT1):c.249CTT[2] (p.Phe85del)

Allele ID
70824
Variant type
Microsatellite
Variant length
3 bp
Cytogenetic location
1p34.2
Genomic location
1: 40092150-40092152 (GRCh38) GRCh38 UCSC
1: 40557822-40557824 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.40557822AAG[2]
NC_000001.11:g.40092150AAG[2]
NG_009192.1:g.10313CTT[2]
... more HGVS
Protein change
F85del
Other names
-
Canonical SPDI
NC_000001.11:40092149:AAGAAGAAG:AAGAAG
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
ClinGen: CA263484
dbSNP: rs386833637
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 3 criteria provided, multiple submitters, no conflicts Jan 4, 2019 RCV000049596.2
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Gene OMIM ClinGen Gene Dosage Sensitivity Curation Variation viewer Related variants
HI score Help TS score Help Within gene All
PPT1 - - GRCh38
GRCh37
407 420

Submitted interpretations and evidence

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Interpretation
(Last evaluated)
Review status
(Assertion criteria)
Condition
(Inheritance)
Submitter More information
Likely pathogenic
(Mar 15, 2016)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 1
Affected status: unknown
Allele origin: unknown
Counsyl
Accession: SCV000485992.1
Submitted: (Nov 23, 2016)
Publications:
PubMed (5)
Likely pathogenic
(Jan 04, 2019)
criteria provided, single submitter
Method: clinical testing
Ceroid lipofuscinosis neuronal 1
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV000946441.1
Submitted: (Mar 28, 2019)
Publications:
PubMed (5)
Comment:
This variant, c.255_257delCTT, results in the deletion of 1 amino acid(s) of the PPT1 protein (p.Phe85del), but otherwise preserves the integrity of the reading frame. … (more)
probable-pathogenic
(-)
no assertion criteria provided
Method: not provided
Ceroid lipofuscinosis neuronal 1
Affected status: not provided
Allele origin: not provided
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM)
Accession: SCV000082003.1
Submitted: (May 19, 2013)
Comment:
FinDis database variant: This variant was not found or characterized by our laboratory, data were collected from public sources: see reference
Comment:
Converted during submission to Likely pathogenic.

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
Update of the mutation spectrum and clinical correlations of over 360 mutations in eight genes that underlie the neuronal ceroid lipofuscinoses. Kousi M Human mutation 2012 PMID: 21990111
Glycosylation, transport, and complex formation of palmitoyl protein thioesterase 1 (PPT1)--distinct characteristics in neurons. Lyly A BMC cell biology 2007 PMID: 17565660
New mutations in the neuronal ceroid lipofuscinosis genes. Mole SE European journal of paediatric neurology : EJPN : official journal of the European Paediatric Neurology Society 2001 PMID: 11589012
Neuronal trafficking of palmitoyl protein thioesterase provides an excellent model to study the effects of different mutations which cause infantile neuronal ceroid lipofuscinocis. Salonen T Molecular and cellular neurosciences 2001 PMID: 11520175
Detection of eight novel palmitoyl protein thioesterase (PPT) mutations underlying infantile neuronal ceroid lipofuscinosis (INCL;CLN1). Salonen T Human mutation 2000 PMID: 10679943
Identification of three novel mutations of the palmitoyl-protein thioesterase-1 (PPT1) gene in children with neuronal ceroid-lipofuscinosis. Waliany S Human mutation 2000 PMID: 10649502

Text-mined citations for rs386833637...

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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 Nov 27, 2021