20-49089552-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 1P and 5B. PP2BP4BS2
The NM_001316.4(CSE1L):c.1987G>A(p.Val663Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000167 in 1,613,950 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 Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )
Consequence
CSE1L
NM_001316.4 missense
NM_001316.4 missense
Scores
1
5
11
Clinical Significance
Conservation
PhyloP100: 9.60
Genes affected
CSE1L (HGNC:2431): (chromosome segregation 1 like) Proteins that carry a nuclear localization signal (NLS) are transported into the nucleus by the importin-alpha/beta heterodimer. Importin-alpha binds the NLS, while importin-beta mediates translocation through the nuclear pore complex. After translocation, RanGTP binds importin-beta and displaces importin-alpha. Importin-alpha must then be returned to the cytoplasm, leaving the NLS protein behind. The protein encoded by this gene binds strongly to NLS-free importin-alpha, and this binding is released in the cytoplasm by the combined action of RANBP1 and RANGAP1. In addition, the encoded protein may play a role both in apoptosis and in cell proliferation. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PP2
?
Missense variant where missense usually causes diseases, CSE1L
BP4
?
Computational evidence support a benign effect (MetaRNN=0.35652816).
BS2
?
High AC in GnomAdExome at 8 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CSE1L | NM_001316.4 | c.1987G>A | p.Val663Ile | missense_variant | 19/25 | ENST00000262982.3 | |
CSE1L | NM_001362762.2 | c.1987G>A | p.Val663Ile | missense_variant | 19/25 | ||
CSE1L | NM_001256135.2 | c.1819G>A | p.Val607Ile | missense_variant | 18/24 | ||
CSE1L | NR_045796.2 | n.1625G>A | non_coding_transcript_exon_variant | 16/22 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CSE1L | ENST00000262982.3 | c.1987G>A | p.Val663Ile | missense_variant | 19/25 | 1 | NM_001316.4 | P1 | |
CSE1L | ENST00000396192.7 | c.1819G>A | p.Val607Ile | missense_variant | 18/24 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251342Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135858
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GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461832Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727218
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.1987G>A (p.V663I) alteration is located in exon 19 (coding exon 18) of the CSE1L gene. This alteration results from a G to A substitution at nucleotide position 1987, causing the valine (V) at amino acid position 663 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Uncertain
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N
REVEL
Benign
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
0.60
.;P
Vest4
MutPred
0.74
.;Loss of catalytic residue at V663 (P = 0.1289);
MVP
MPC
0.43
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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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