NM_001042432.2:c.*205G>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001042432.2(CLN3):c.*205G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
CLN3
NM_001042432.2 3_prime_UTR
NM_001042432.2 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.897
Publications
0 publications found
Genes affected
CLN3 (HGNC:2074): (CLN3 lysosomal/endosomal transmembrane protein, battenin) This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
CLN3 Gene-Disease associations (from GenCC):
- inherited retinal dystrophyInheritance: AR Classification: DEFINITIVE Submitted by: G2P
- neuronal ceroid lipofuscinosisInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- neuronal ceroid lipofuscinosis 3Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Genomics England PanelApp, G2P, Labcorp Genetics (formerly Invitae), Myriad Women’s Health
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.84).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLN3 | NM_001042432.2 | c.*205G>T | 3_prime_UTR_variant | Exon 16 of 16 | ENST00000636147.2 | NP_001035897.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLN3 | ENST00000636147.2 | c.*205G>T | 3_prime_UTR_variant | Exon 16 of 16 | 1 | NM_001042432.2 | ENSP00000490105.1 | |||
ENSG00000261832 | ENST00000637378.1 | c.228+4794G>T | intron_variant | Intron 4 of 9 | 5 | ENSP00000490831.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 488770Hom.: 0 Cov.: 6 AF XY: 0.00 AC XY: 0AN XY: 257448
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
488770
Hom.:
Cov.:
6
AF XY:
AC XY:
0
AN XY:
257448
African (AFR)
AF:
AC:
0
AN:
13470
American (AMR)
AF:
AC:
0
AN:
22054
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
14798
East Asian (EAS)
AF:
AC:
0
AN:
30808
South Asian (SAS)
AF:
AC:
0
AN:
49446
European-Finnish (FIN)
AF:
AC:
0
AN:
29868
Middle Eastern (MID)
AF:
AC:
0
AN:
2092
European-Non Finnish (NFE)
AF:
AC:
0
AN:
298992
Other (OTH)
AF:
AC:
0
AN:
27242
GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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