NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del) AND Neuronal ceroid lipofuscinosis

Germline classification:: Pathogenic (2 submissions)
Last evaluated:: Jan 22, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

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:: RCV000989353.17

Allele description [Variation Report for NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del)]

NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del)

Gene:

CLN6:CLN6 transmembrane ER protein [Gene - OMIM - HGNC]

Variant type:

Microsatellite

Cytogenetic location:

15q23

Genomic location:

Preferred name:

NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del)

HGVS:

NC_000015.10:g.68208282GAG[1]
NC_000015.9:g.68500618_68500620del
NG_008764.2:g.53927CCT[1]
NM_017882.3:c.791CCT[1]MANE SELECT
NP_060352.1:p.Ser265del
LRG_832t1:c.791CCT[1]
LRG_832:g.53927CCT[1]
LRG_832p1:p.Ser265del
NC_000015.9:g.68500618_68500620del
NC_000015.9:g.68500618_68500620delAGG
NC_000015.9:g.68500620GAG[1]
NM_017882.2:c.794_796delCCT
NM_017882.3:c.794_796delMANE SELECT
p.S265del
p.Ser265del

Protein change:

S265del

Links:

dbSNP: rs768422260

NCBI 1000 Genomes Browser:

rs768422260

Molecular consequence:

NM_017882.3:c.791CCT[1] - inframe_deletion - [Sequence Ontology: SO:0001822]

Functional consequence:

probably has functional consequence

Condition(s)

Name:: Neuronal ceroid lipofuscinosis
Synonyms:: Ceroid storage disease
Identifiers:: MONDO: MONDO:0016295; MedGen: C0027877; Orphanet: 79263; OMIM: PS256730

Recent activity

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hypothetical protein HOQ89_gp069 [Lactobacillus phage ATCC 8014-B2]
hypothetical protein HOQ89_gp069 [Lactobacillus phage ATCC 8014-B2]
gi|1841996189|ref|YP_009784035.1|

Protein
SRX302570 (1)
SRA
SRP005712 (35)
SRA
822377[uid] AND (alive[prop]) (1)
Gene
RNA-binding CRS1 / YhbY (CRM) domain protein [Arabidopsis thaliana]
RNA-binding CRS1 / YhbY (CRM) domain protein [Arabidopsis thaliana]
Gene ID:822377

Gene

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001139644	Mendelics	criteria provided, single submitter (Mendelics Assertion Criteria 2017)	Pathogenic (May 28, 2019)	unknown	clinical testing	Citation Link,
SCV001410001	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Jan 22, 2024)	germline	clinical testing	PubMed (6) [See all records that cite these PMIDs] 19135028, 19520283, 30705896, 31029456, 15265688, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001139644

Mendelics

criteria provided, single submitter

(Mendelics Assertion Criteria 2017)

Pathogenic
(May 28, 2019)

unknown

clinical testing

Citation Link,

SCV001410001

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Jan 22, 2024)

germline

clinical testing

PubMed (6)
[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
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Variant late infantile ceroid lipofuscinoses associated with novel mutations in CLN6.

Cannelli N, Garavaglia B, Simonati A, Aiello C, Barzaghi C, Pezzini F, Cilio MR, Biancheri R, Morbin M, Dalla Bernardina B, Granata T, Tessa A, Invernizzi F, Pessagno A, Boldrini R, Zibordi F, Grazian L, Claps D, Carrozzo R, Mole SE, Nardocci N, Santorelli FM.

Biochem Biophys Res Commun. 2009 Feb 20;379(4):892-7. doi: 10.1016/j.bbrc.2008.12.159. Epub 2009 Jan 7.

PubMed [citation]

PMID:: 19135028

Variant late infantile neuronal ceroid lipofuscinosis (CLN6 gene) in Saudi Arabia.

Al-Muhaizea MA, Al-Hassnan ZN, Chedrawi A.

Pediatr Neurol. 2009 Jul;41(1):74-6. doi: 10.1016/j.pediatrneurol.2009.01.012. Review.

PubMed [citation]

PMID:: 19520283

See all PubMed Citations (6)

Details of each submission

From Mendelics, SCV001139644.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001410001.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (6)

Description

This variant, c.794_796del, results in the deletion of 1 amino acid(s) of the CLN6 protein (p.Ser265del), but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs768422260, gnomAD 0.01%). This variant has been observed in individuals with neuronal ceroid lipofuscinosis type 6 (PMID: 19135028, 19520283, 30705896, 31029456). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 205182). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CLN6 function (PMID: 15265688). For these reasons, this variant has been classified as Pathogenic.

#	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: Oct 13, 2024

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