8-1780485-C-T
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 4P and 5B. PM1PM2BP4_StrongBS1_Supporting
The NM_018941.4(CLN8):c.779C>T(p.Pro260Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000159 in 1,614,194 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: 𝑓 0.00066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00011 ( 0 hom. )
Consequence
CLN8
NM_018941.4 missense
NM_018941.4 missense
Scores
2
12
4
Clinical Significance
Conservation
PhyloP100: 5.65
Genes affected
CLN8 (HGNC:2079): (CLN8 transmembrane ER and ERGIC protein) This gene encodes a transmembrane protein belonging to a family of proteins containing TLC domains, which are postulated to function in lipid synthesis, transport, or sensing. The protein localizes to the endoplasmic reticulum (ER), and may recycle between the ER and ER-Golgi intermediate compartment. Mutations in this gene are associated with a disorder characterized by progressive epilepsy with cognitive disabilities (EPMR), which is a subtype of neuronal ceroid lipofuscinoses (NCL). Patients with mutations in this gene have altered levels of sphingolipid and phospholipids in the brain. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PM1
In a domain TLC (size 200) in uniprot entity CLN8_HUMAN there are 17 pathogenic changes around while only 5 benign (77%) in NM_018941.4
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.017316312).
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.000657 (100/152304) while in subpopulation AFR AF= 0.00219 (91/41564). AF 95% confidence interval is 0.00183. There are 0 homozygotes in gnomad4. There are 44 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLN8 | NM_018941.4 | c.779C>T | p.Pro260Leu | missense_variant | Exon 3 of 3 | ENST00000331222.6 | NP_061764.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLN8 | ENST00000331222.6 | c.779C>T | p.Pro260Leu | missense_variant | Exon 3 of 3 | 1 | NM_018941.4 | ENSP00000328182.4 | ||
KBTBD11-OT1 | ENST00000635855.1 | n.543+8888C>T | intron_variant | Intron 2 of 29 | 5 | ENSP00000489726.1 |
Frequencies
GnomAD3 genomes AF: 0.000651 AC: 99AN: 152186Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000227 AC: 57AN: 251410Hom.: 0 AF XY: 0.000132 AC XY: 18AN XY: 135878
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GnomAD4 exome AF: 0.000107 AC: 157AN: 1461890Hom.: 0 Cov.: 32 AF XY: 0.0000811 AC XY: 59AN XY: 727244
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GnomAD4 genome AF: 0.000657 AC: 100AN: 152304Hom.: 0 Cov.: 33 AF XY: 0.000591 AC XY: 44AN XY: 74478
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:7Benign:3
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
not provided Uncertain:4
Uncertain significance, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Uncertain significance, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, Amsterdam University Medical Center | - | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Mayo Clinic Laboratories, Mayo Clinic | Apr 21, 2023 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Aug 07, 2024 | Reported previously with a second variant in a patient with malnutrition, developmental delay, absent speech, severe intellectual disability, epilepsy, and cerebellar and cerebral atrophy (PMID: 38751748); Reported previously with a second variant in siblings with adult-onset nyctalopia (PMID: 36912596); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 36912596, 38751748) - |
Neuronal ceroid lipofuscinosis 8;C1864923:Neuronal ceroid lipofuscinosis 8 northern epilepsy variant Pathogenic:1Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago | Nov 11, 2021 | CLN8 NM_018941 exon 3 p.Pro260Leu (c.779C>T): This variant has not been reported in the literature but is present in 64/24030 African individuals in the Genome Aggregation Database (http://gnomad.broadinstitute.org/rs146579299). This variant is present in ClinVar (Variation ID:205196). Evolutionary conservation and computational predictive tools for this variant are unclear. In summary, data on this variant is insufficient for disease classification. Therefore, the clinical significance of this variant is uncertain. - |
Likely pathogenic, flagged submission | clinical testing | Bioinformatics Unit, Institut Pasteur de Montevideo | Feb 29, 2024 | The two variants found can be classified as likely pathogenic according to ACMG criteria: i. Pro260Leu missense variant has low frequency (PM2), detected in trans with another likely pathogenic mutation (PM3), is a missense variant in a gene where missense variants are a common mechanism of disease (PP2). Additionally, multiple lines of evidence of computational in silico scores support a deleterious effect (PP3), the patient's phenotype is highly specific for a disease with a single gene etiology (PP4). Hence, 2 PM and 3 PP, leads to a likely pathogenic classification; ii. Val261Ala missense variant can also be classified as likely pathogenic with the same rules applied. We have identified the two variants in compound heterozygosity with additional data to consider them as likely pathogenic mutations. - |
not specified Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Mendelics | May 04, 2022 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Aug 05, 2024 | Variant summary: CLN8 c.779C>T (p.Pro260Leu) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.00023 in 251410 control chromosomes, predominantly at a frequency of 0.0026 within the African or African-American subpopulation in the gnomAD database. The observed variant frequency within African or African-American control individuals in the gnomAD database is approximately 3 fold of the estimated maximal expected allele frequency for a pathogenic variant in CLN8 causing Neuronal Ceroid-Lipofuscinosis (Batten Disease) phenotype (0.00087). c.779C>T has been reported in the literature in two individuals affected with retinal dystrophy, without strong evidence for causality (Kolesnikova_2023). These report(s) do not provide unequivocal conclusions about association of the variant with Neuronal Ceroid-Lipofuscinosis (Batten Disease). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publication has been ascertained in the context of this evaluation (PMID: 36912596). ClinVar contains an entry for this variant (Variation ID: 205196). Based on the evidence outlined above, the variant was classified as likely benign. - |
Neuronal ceroid lipofuscinosis 8 Uncertain:1
Uncertain significance, no assertion criteria provided | clinical testing | Natera, Inc. | Jun 25, 2020 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 05, 2024 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Neuronal ceroid lipofuscinosis Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 27, 2025 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T;T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;M;M;M;M
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;.;.;.;.
REVEL
Uncertain
Sift
Pathogenic
D;.;.;.;.
Sift4G
Uncertain
D;.;.;.;.
Polyphen
P;P;P;P;P
Vest4
MVP
MPC
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at