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NM_000310.4(PPT1):c.628-2A>G

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Interpretation:
Likely pathogenic​

Review status:
criteria provided, single submitter
Submissions:
1 (Most recent: Jan 7, 2021)
Last evaluated:
Aug 27, 2020
Accession:
VCV001067368.1
Variation ID:
1067368
Description:
single nucleotide variant
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NM_000310.4(PPT1):c.628-2A>G

Allele ID
1054839
Variant type
single nucleotide variant
Variant length
1 bp
Cytogenetic location
1p34.2
Genomic location
1: 40078660 (GRCh38) GRCh38 UCSC
1: 40544332 (GRCh37) GRCh37 UCSC
HGVS
Nucleotide Protein Molecular
consequence
NC_000001.10:g.40544332T>C
NC_000001.11:g.40078660T>C
NG_009192.1:g.23811A>G
... more HGVS
Protein change
-
Other names
-
Canonical SPDI
NC_000001.11:40078659:T:C
Functional consequence
-
Global minor allele frequency (GMAF)
-

Allele frequency
-
Links
VarSome
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Aggregate interpretations per condition

Interpreted condition Interpretation Number of submissions Review status Last evaluated Variation/condition record
Likely pathogenic 1 criteria provided, single submitter Aug 27, 2020 RCV001378615.1
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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
(Aug 27, 2020)
criteria provided, single submitter
Method: clinical testing
Neuronal ceroid lipofuscinosis 1
Affected status: unknown
Allele origin: germline
Invitae
Accession: SCV001576219.1
Submitted: (Jan 07, 2021)
Publications:
PubMed (3)
PubMed: 161995471067994321990111
Comment:
This sequence change affects an acceptor splice site in intron 6 of the PPT1 gene. It is expected to disrupt RNA splicing and likely results … (more)

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
Splicing in action: assessing disease causing sequence changes. Baralle D Journal of medical genetics 2005 PMID: 16199547
Detection of eight novel palmitoyl protein thioesterase (PPT) mutations underlying infantile neuronal ceroid lipofuscinosis (INCL;CLN1). Salonen T Human mutation 2000 PMID: 10679943

Record last updated Oct 08, 2021