Genetic Variant JPT2:p.Pro5Gln (chr16-1678326-C-A) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_144570.3(JPT2):c.14C>A(p.Pro5Gln) 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. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P5R) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

JPT2
NM_144570.3 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 1.02

Publications

0 publications found

Variant links:

Genes affected

JPT2 (HGNC:14137): (Jupiter microtubule associated homolog 2) Located in cytosol and plasma membrane. [provided by Alliance of Genome Resources, Apr 2022]

JPT2 links:

ENSG00000261732 (HGNC:):

ENSG00000261732 links:

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (MetaRNN=0.18197972).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_144570.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
JPT2	NM_144570.3	MANE Select	c.14C>A	p.Pro5Gln	missense	Exon 1 of 5	NP_653171.1	Q9H910-1
JPT2	NM_001434664.1		c.14C>A	p.Pro5Gln	missense	Exon 1 of 7	NP_001421593.1
JPT2	NM_001434665.1		c.14C>A	p.Pro5Gln	missense	Exon 1 of 6	NP_001421594.1	Q9H910-3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
JPT2	ENST00000248098.8	TSL:1 MANE Select	c.14C>A	p.Pro5Gln	missense	Exon 1 of 5	ENSP00000248098.3	Q9H910-1
JPT2	ENST00000561516.5	TSL:1	c.14C>A	p.Pro5Gln	missense	Exon 1 of 4	ENSP00000454459.1	H3BMM8
JPT2	ENST00000569256.5	TSL:1	n.71C>A		non_coding_transcript_exon	Exon 1 of 4

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

1084640

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

512746

African (AFR)

AF:

0.00

AC:

AN:

22760

American (AMR)

AF:

0.00

AC:

AN:

8796

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14190

East Asian (EAS)

AF:

0.00

AC:

AN:

26312

South Asian (SAS)

AF:

0.00

AC:

AN:

19682

European-Finnish (FIN)

AF:

0.00

AC:

AN:

26360

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3634

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

919380

Other (OTH)

AF:

0.00

AC:

AN:

43526

GnomAD4 genome

Cov.:

ClinVar

ClinVar submissions

Significance:Uncertain significance

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.096

BayesDel_addAF

Benign

-0.076

BayesDel_noAF

Benign

-0.35

CADD

Benign

(source)

DANN

Benign

0.96

DEOGEN2

Benign

0.024

Eigen

Benign

-0.33

Eigen_PC

Benign

-0.57

FATHMM_MKL

Benign

0.35

LIST_S2

Benign

0.44

M_CAP

Pathogenic

0.30

MetaRNN

Benign

0.18

MetaSVM

Benign

-0.95

PhyloP100

1.0

PrimateAI

Uncertain

0.61

PROVEAN

Benign

-1.5

REVEL

Benign

0.060

Sift

Benign

0.044

Sift4G

Uncertain

0.046

Polyphen

0.73

Vest4

0.18

MutPred

0.24

Gain of sheet (P = 0.0085)

MVP

0.10

MPC

0.78

ClinPred

0.59

GERP RS

-0.047

PromoterAI

-0.18

Neutral

(source)

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Varity_R

0.072

gMVP

0.21

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

ClinVar

Computational scores

Splicing

Publications

Other links and lift over