rs1071705

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_002532.6(NUP88):​c.2157A>T​(p.Lys719Asn) variant causes a missense 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)

Consequence

NUP88
NM_002532.6 missense

Scores

1
6
9

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0130
Variant links:
Genes affected
NUP88 (HGNC:8067): (nucleoporin 88) The nuclear pore complex is a massive structure that extends across the nuclear envelope, forming a gateway that regulates the flow of macromolecules between the nucleus and the cytoplasm. Nucleoporins, a family of 50 to 100 proteins, are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene belongs to the nucleoporin family and is associated with the oncogenic nucleoporin CAN/Nup214 in a dynamic subcomplex. This protein is also overexpressed in a large number of malignant neoplasms and precancerous dysplasias. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2016]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.3159722).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NUP88NM_002532.6 linkc.2157A>T p.Lys719Asn missense_variant Exon 16 of 17 ENST00000573584.6 NP_002523.2 Q99567
NUP88NM_001320653.2 linkc.2205A>T p.Lys735Asn missense_variant Exon 16 of 17 NP_001307582.1 Q99567J3KMX1B4DP20
NUP88XM_047436155.1 linkc.1812A>T p.Lys604Asn missense_variant Exon 16 of 17 XP_047292111.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NUP88ENST00000573584.6 linkc.2157A>T p.Lys719Asn missense_variant Exon 16 of 17 1 NM_002532.6 ENSP00000458954.1 Q99567

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
29
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
0.72
BayesDel_addAF
Benign
-0.24
T
BayesDel_noAF
Benign
-0.58
CADD
Benign
19
DANN
Uncertain
1.0
DEOGEN2
Benign
0.040
T
Eigen
Benign
-0.47
Eigen_PC
Benign
-0.37
FATHMM_MKL
Uncertain
0.79
D
LIST_S2
Uncertain
0.89
D
M_CAP
Benign
0.026
D
MetaRNN
Benign
0.32
T
MetaSVM
Benign
-0.99
T
MutationAssessor
Uncertain
2.0
M
PrimateAI
Uncertain
0.61
T
Sift4G
Uncertain
0.0050
D
Polyphen
0.049
B
Vest4
0.50
MutPred
0.59
Loss of ubiquitination at K719 (P = 0.0148);
MVP
0.50
MPC
0.48
ClinPred
0.81
D
GERP RS
3.5
Varity_R
0.12
gMVP
0.45

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1071705; hg19: chr17-5290033; API