11-66563989-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003793.4(CTSF):c.1399C>T(p.Arg467Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000105 in 1,613,658 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★★). Synonymous variant affecting the same amino acid position (i.e. R467R) has been classified as Benign.
Frequency
Consequence
NM_003793.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTSF | NM_003793.4 | c.1399C>T | p.Arg467Cys | missense_variant | 13/13 | ENST00000310325.10 | NP_003784.2 | |
CTSF | XM_011545328.3 | c.1219C>T | p.Arg407Cys | missense_variant | 13/13 | XP_011543630.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTSF | ENST00000310325.10 | c.1399C>T | p.Arg467Cys | missense_variant | 13/13 | 1 | NM_003793.4 | ENSP00000310832.5 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250654Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135716
GnomAD4 exome AF: 0.0000109 AC: 16AN: 1461492Hom.: 0 Cov.: 33 AF XY: 0.00000963 AC XY: 7AN XY: 727062
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152166Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74336
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 20, 2023 | The c.1399C>T (p.R467C) alteration is located in exon 13 (coding exon 13) of the CTSF gene. This alteration results from a C to T substitution at nucleotide position 1399, causing the arginine (R) at amino acid position 467 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Neuronal ceroid lipofuscinosis 13 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Institute of Human Genetics, University of Leipzig Medical Center | Jan 03, 2023 | _x000D_This variant was identified as compound heterozygous with NM_003793.4:c.1069T>C. Criteria applied: PM2_SUP, PP3 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at