NM_000391.4(TPP1):c.889C>T (p.Arg297Trp) AND Neuronal ceroid lipofuscinosis 2

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Apr 20, 2022
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:: RCV001836218.2

Allele description [Variation Report for NM_000391.4(TPP1):c.889C>T (p.Arg297Trp)]

NM_000391.4(TPP1):c.889C>T (p.Arg297Trp)

Gene:

TPP1:tripeptidyl peptidase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

11p15.4

Genomic location:

Preferred name:

NM_000391.4(TPP1):c.889C>T (p.Arg297Trp)

HGVS:

NC_000011.10:g.6616501G>A
NG_008653.1:g.7961C>T
NM_000391.4:c.889C>TMANE SELECT
NP_000382.3:p.Arg297Trp
LRG_830t1:c.889C>T
LRG_830:g.7961C>T
LRG_830p1:p.Arg297Trp
NC_000011.9:g.6637732G>A
NM_000391.3:c.889C>T

Protein change:

R297W

Links:

dbSNP: rs553122824

NCBI 1000 Genomes Browser:

rs553122824

Molecular consequence:

NM_000391.4:c.889C>T - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Neuronal ceroid lipofuscinosis 2
Synonyms:: JANSKY-BIELSCHOWSKY DISEASE NEURONAL CEROID LIPOFUSCINOSIS, LATE INFANTILE; TPP1-Related Neuronal Ceroid-Lipofuscinosis
Identifiers:: MONDO: MONDO:0008769; MedGen: C1876161; Orphanet: 168491; Orphanet: 228349; Orphanet: 79264; OMIM: 204500

Recent activity

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OMIM Links for Gene (Select 7739) (1)
OMIM
PREDICTED: Homo sapiens zinc finger protein 185 with LIM domain (ZNF185), transc...
PREDICTED: Homo sapiens zinc finger protein 185 with LIM domain (ZNF185), transcript variant X46, mRNA
gi|2462499740|ref|XM_054333392.1|

Nucleotide
PREDICTED: Homo sapiens zinc finger protein 185 with LIM domain (ZNF185), transc...
PREDICTED: Homo sapiens zinc finger protein 185 with LIM domain (ZNF185), transcript variant X36, mRNA
gi|2217394689|ref|XM_005274745.3|

Nucleotide
JGI_XZT63291.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7637770 5'...
JGI_XZT63291.fwd NIH_XGC_tropTad5 Xenopus tropicalis cDNA clone IMAGE:7637770 5', mRNA sequence
gi|74301601|gnl|dbEST|31377127|gb|C 14.2|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002094844	Natera, Inc.	no assertion criteria provided	Uncertain significance (Mar 2, 2021)	germline	clinical testing
SCV002577581	Laboratory of Medical Genetics, National & Kapodistrian University of Athens	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Apr 20, 2022)	paternal	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002094844

Natera, Inc.

no assertion criteria provided

Uncertain significance
(Mar 2, 2021)

germline

clinical testing

SCV002577581

Laboratory of Medical Genetics, National & Kapodistrian University of Athens

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Apr 20, 2022)

paternal

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	paternal	yes	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Natera, Inc., SCV002094844.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	not provided

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Laboratory of Medical Genetics, National & Kapodistrian University of Athens, SCV002577581.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

Description

PVS1, PM2, PP3

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	paternal	yes	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Sep 29, 2024

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