NM_000310.4(PPT1):c.316C>T (p.Gln106Ter) AND Neuronal ceroid lipofuscinosis 1

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Mar 16, 2023
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:: RCV003619909.1

Allele description [Variation Report for NM_000310.4(PPT1):c.316C>T (p.Gln106Ter)]

NM_000310.4(PPT1):c.316C>T (p.Gln106Ter)

Gene:

PPT1:palmitoyl-protein thioesterase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p34.2

Genomic location:

Preferred name:

NM_000310.4(PPT1):c.316C>T (p.Gln106Ter)

HGVS:

NC_000001.11:g.40092091G>A
NG_009192.1:g.10380C>T
NM_000310.4:c.316C>TMANE SELECT
NM_001142604.2:c.125-2579C>T
NM_001363695.2:c.316C>T
NP_000301.1:p.Gln106Ter
NP_000301.1:p.Gln106Ter
NP_001350624.1:p.Gln106Ter
LRG_690t1:c.316C>T
LRG_690:g.10380C>T
LRG_690p1:p.Gln106Ter
NC_000001.10:g.40557763G>A
NM_000310.3:c.316C>T

Protein change:

Q106*

Molecular consequence:

NM_001142604.2:c.125-2579C>T - intron variant - [Sequence Ontology: SO:0001627]
NM_000310.4:c.316C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001363695.2:c.316C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Name:: Neuronal ceroid lipofuscinosis 1 (CLN1)
Synonyms:: CEROID LIPOFUSCINOSIS, NEURONAL, 1, VARIABLE AGE AT ONSET; CLN1 variable age at onset; Infantile CLN (type of CLN1); See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009744; MedGen: C1850451; OMIM: 256730

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004375110	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Mar 16, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 33486620, 10679943, 21990111, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004375110

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Mar 16, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Citations

PubMed

Neuronal ceroid lipofuscinosis: genetic and phenotypic spectrum of 14 patients from Turkey.

Kose M, Kose E, Ünalp A, Yılmaz Ü, Edizer S, Tekin HG, Karaoğlu P, Özdemir TR, Er E, Onay H, Yildirim ES.

Neurol Sci. 2021 Mar;42(3):1103-1111. doi: 10.1007/s10072-021-05067-8. Epub 2021 Jan 23.

PubMed [citation]

PMID:: 33486620

Detection of eight novel palmitoyl protein thioesterase (PPT) mutations underlying infantile neuronal ceroid lipofuscinosis (INCL;CLN1).

Salonen T, Järvelä I, Peltonen L, Jalanko A.

Hum Mutat. 2000;15(3):273-9.

PubMed [citation]

PMID:: 10679943

See all PubMed Citations (4)

Details of each submission

From Invitae, SCV004375110.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This premature translational stop signal has been observed in individual(s) with neuronal ceroid lipofuscinosis (PMID: 33486620). This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Gln106*) in the PPT1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PPT1 are known to be pathogenic (PMID: 10679943, 21990111).

#	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

Last Updated: Feb 28, 2024

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