NM_015231.3:c.949A>G

Variant names:

Variant summary

Our verdict is Benign. The variant received -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_015231.3(NUP160):c.949A>G(p.Thr317Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.432 in 1,601,690 control chromosomes in the GnomAD database, including 155,576 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.35 ( 10722 hom., cov: 32)

Exomes 𝑓: 0.44 ( 144854 hom. )

Consequence

NUP160
NM_015231.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:4

Conservation

PhyloP100: 0.707

Publications

44 publications found

Variant links:

Genes affected

NUP160 (HGNC:18017): (nucleoporin 160) A structural constituent of nuclear pore. Involved in mRNA export from nucleus and nephron development. Part of nuclear pore outer ring. Colocalizes with kinetochore. Implicated in nephrotic syndrome type 19. [provided by Alliance of Genome Resources, Apr 2022]

NUP160 Gene-Disease associations (from GenCC):

nephrotic syndrome, type 19
Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
familial idiopathic steroid-resistant nephrotic syndrome
Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

NUP160 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=4.3421984E-4).

BP6

Variant 11-47835701-T-C is Benign according to our data. Variant chr11-47835701-T-C is described in ClinVar as Benign. ClinVar VariationId is 1327016.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.506 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NUP160	NM_015231.3 link	c.949A>G	p.Thr317Ala	missense_variant	Exon 7 of 36	ENST00000378460.7	NP_056046.2	Q12769
NUP160	NR_134636.3 link	n.981A>G		non_coding_transcript_exon_variant	Exon 7 of 36

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NUP160	ENST00000378460.7 link	c.949A>G	p.Thr317Ala	missense_variant	Exon 7 of 36	1	NM_015231.3	ENSP00000367721.3		A0A8V8NBT1

Frequencies

GnomAD3 genomes

AF:

0.349

AC:

53077

AN:

151886

Hom.:

10723

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.330

Gnomad ASJ

AF:

0.502

Gnomad EAS

AF:

0.393

Gnomad SAS

AF:

0.523

Gnomad FIN

AF:

0.341

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.452

Gnomad OTH

AF:

0.407

GnomAD2 exomes

AF:

0.408

AC:

98682

AN:

241994

AF XY:

0.425

show subpopulations

Gnomad AFR exome

AF:

0.152

Gnomad AMR exome

AF:

0.250

Gnomad ASJ exome

AF:

0.496

Gnomad EAS exome

AF:

0.393

Gnomad FIN exome

AF:

0.352

Gnomad NFE exome

AF:

0.459

Gnomad OTH exome

AF:

0.433

GnomAD4 exome

AF:

0.440

AC:

638219

AN:

1449690

Hom.:

144854

Cov.:

AF XY:

0.445

AC XY:

320488

AN XY:

720578

show subpopulations

African (AFR)

AF:

0.139

AC:

4599

AN:

33146

American (AMR)

AF:

0.260

AC:

11267

AN:

43256

Ashkenazi Jewish (ASJ)

AF:

0.502

AC:

13007

AN:

25914

East Asian (EAS)

AF:

0.325

AC:

12707

AN:

39090

South Asian (SAS)

AF:

0.535

AC:

44598

AN:

83374

European-Finnish (FIN)

AF:

0.361

AC:

19235

AN:

53268

Middle Eastern (MID)

AF:

0.449

AC:

2586

AN:

5762

European-Non Finnish (NFE)

AF:

0.456

AC:

504072

AN:

1105952

Other (OTH)

AF:

0.436

AC:

26148

AN:

59928

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.469

Heterozygous variant carriers

16060

32119

48179

64238

80298

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

14974

29948

44922

59896

74870

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.349

AC:

53073

AN:

152000

Hom.:

10722

Cov.:

AF XY:

0.346

AC XY:

25678

AN XY:

74298

show subpopulations

African (AFR)

AF:

0.151

AC:

6261

AN:

41478

American (AMR)

AF:

0.330

AC:

5035

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.502

AC:

1740

AN:

3468

East Asian (EAS)

AF:

0.393

AC:

2027

AN:

5164

South Asian (SAS)

AF:

0.523

AC:

2521

AN:

4822

European-Finnish (FIN)

AF:

0.341

AC:

3597

AN:

10544

Middle Eastern (MID)

AF:

0.367

AC:

108

AN:

294

European-Non Finnish (NFE)

AF:

0.452

AC:

30696

AN:

67952

Other (OTH)

AF:

0.403

AC:

852

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1651

3302

4954

6605

8256

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

528

1056

1584

2112

2640

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.425

Hom.:

43342

Bravo

AF:

0.336

TwinsUK

AF:

0.454

AC:

1682

ALSPAC

AF:

0.449

AC:

1730

ESP6500AA

AF:

0.158

AC:

697

ESP6500EA

AF:

0.459

AC:

3945

ExAC

AF:

0.412

AC:

50044

Asia WGS

AF:

0.472

AC:

1639

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:4

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Feb 03, 2025

Labcorp Genetics (formerly Invitae), Labcorp

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Breakthrough Genomics, Breakthrough Genomics

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:not provided

- -

NUP160-related disorder

Benign:1

Jul 18, 2019

PreventionGenetics, part of Exact Sciences

Significance:Benign

Review Status:no assertion criteria provided

Collection Method:clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Nephrotic syndrome, type 19

Benign:1

Sep 05, 2021

Genome-Nilou Lab

Significance:Benign

Review Status:criteria provided, single submitter

Collection Method:clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.054

BayesDel_addAF

Benign

-0.76

BayesDel_noAF

Benign

-0.72

CADD

Benign

(source)

DANN

Benign

0.82

DEOGEN2

Benign

0.026

Eigen

Benign

-1.0

Eigen_PC

Benign

-0.87

FATHMM_MKL

Uncertain

0.81

MetaRNN

Benign

0.00043

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.90

PhyloP100

0.71

PrimateAI

Benign

0.27

PROVEAN

Benign

-1.1

REVEL

Benign

0.081

Sift

Benign

0.19

Sift4G

Uncertain

0.028

Polyphen

0.0

Vest4

0.052

MPC

0.20

ClinPred

0.0025

GERP RS

0.28

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.031

gMVP

0.094

Mutation Taster

=91/9

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over