rs150565530

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_024923.4(NUP210):​c.5341G>A​(p.Val1781Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000248 in 1,614,126 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: 𝑓 0.000026 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000025 ( 0 hom. )

Consequence

NUP210
NM_024923.4 missense

Scores

8
11

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.28
Variant links:
Genes affected
NUP210 (HGNC:30052): (nucleoporin 210) 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 are the main components of the nuclear pore complex in eukaryotic cells. The protein encoded by this gene is a membrane-spanning glycoprotein that is a major component of the nuclear pore complex. Multiple pseudogenes related to this gene are located on chromosome 3. [provided by RefSeq, Jul 2013]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NUP210NM_024923.4 linkc.5341G>A p.Val1781Met missense_variant Exon 37 of 40 ENST00000254508.7 NP_079199.2 Q8TEM1-1
NUP210XM_047447795.1 linkc.2725G>A p.Val909Met missense_variant Exon 19 of 22 XP_047303751.1
NUP210XM_047447797.1 linkc.2692G>A p.Val898Met missense_variant Exon 19 of 22 XP_047303753.1
NUP210XM_047447796.1 linkc.2656G>A p.Val886Met missense_variant Exon 19 of 22 XP_047303752.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NUP210ENST00000254508.7 linkc.5341G>A p.Val1781Met missense_variant Exon 37 of 40 2 NM_024923.4 ENSP00000254508.5 Q8TEM1-1
NUP210ENST00000695489.1 linkn.1069G>A non_coding_transcript_exon_variant Exon 1 of 4
NUP210ENST00000695490.1 linkn.*769G>A non_coding_transcript_exon_variant Exon 19 of 22 ENSP00000511960.1 A0A8Q3WKI1
NUP210ENST00000695490.1 linkn.*769G>A 3_prime_UTR_variant Exon 19 of 22 ENSP00000511960.1 A0A8Q3WKI1

Frequencies

GnomAD3 genomes
AF:
0.0000263
AC:
4
AN:
152240
Hom.:
0
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000441
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000239
AC:
6
AN:
251374
Hom.:
0
AF XY:
0.0000294
AC XY:
4
AN XY:
135890
show subpopulations
Gnomad AFR exome
AF:
0.0000615
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000352
Gnomad OTH exome
AF:
0.000163
GnomAD4 exome
AF:
0.0000246
AC:
36
AN:
1461886
Hom.:
0
Cov.:
60
AF XY:
0.0000248
AC XY:
18
AN XY:
727240
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000315
Gnomad4 OTH exome
AF:
0.0000166
GnomAD4 genome
AF:
0.0000263
AC:
4
AN:
152240
Hom.:
0
Cov.:
34
AF XY:
0.0000269
AC XY:
2
AN XY:
74382
show subpopulations
Gnomad4 AFR
AF:
0.0000241
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000441
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000450
Hom.:
0
Bravo
AF:
0.0000189
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.000116
AC:
1
ExAC
AF:
0.00000824
AC:
1
EpiCase
AF:
0.0000545
EpiControl
AF:
0.00

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Feb 12, 2025
Ambry Genetics
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

The c.5341G>A (p.V1781M) alteration is located in exon 37 (coding exon 37) of the NUP210 gene. This alteration results from a G to A substitution at nucleotide position 5341, causing the valine (V) at amino acid position 1781 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.38
BayesDel_addAF
Benign
-0.058
T
BayesDel_noAF
Benign
-0.21
CADD
Benign
23
DANN
Uncertain
0.99
DEOGEN2
Benign
0.20
T
Eigen
Benign
0.11
Eigen_PC
Benign
0.092
FATHMM_MKL
Uncertain
0.93
D
LIST_S2
Benign
0.84
T
M_CAP
Benign
0.045
D
MetaRNN
Uncertain
0.63
D
MetaSVM
Benign
-1.1
T
MutationAssessor
Uncertain
2.7
M
PrimateAI
Uncertain
0.65
T
PROVEAN
Benign
-1.5
N
REVEL
Benign
0.21
Sift
Uncertain
0.0020
D
Sift4G
Uncertain
0.0040
D
Polyphen
0.65
P
Vest4
0.69
MVP
0.34
MPC
0.47
ClinPred
0.64
D
GERP RS
4.8
Varity_R
0.17
gMVP
0.85

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: rs150565530; hg19: chr3-13361305; API