Genetic Variant NM_002435.3:c.10C>T (chr15-74890083-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2

The NM_002435.3(MPI):c.10C>T(p.Pro4Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00141 in 1,607,936 control chromosomes in the GnomAD database, including 13 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Synonymous variant affecting the same amino acid position (i.e. P4P) has been classified as Uncertain significance.

Frequency

Genomes: 𝑓 0.0014 ( 1 hom., cov: 33)

Exomes 𝑓: 0.0014 ( 12 hom. )

Consequence

MPI
NM_002435.3 missense

Scores

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:2B:10

Conservation

PhyloP100: 1.18

Publications

9 publications found

Variant links:

Genes affected

MPI (HGNC:7216): (mannose phosphate isomerase) Phosphomannose isomerase catalyzes the interconversion of fructose-6-phosphate and mannose-6-phosphate and plays a critical role in maintaining the supply of D-mannose derivatives, which are required for most glycosylation reactions. Mutations in the MPI gene were found in patients with carbohydrate-deficient glycoprotein syndrome, type Ib. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]

MPI Gene-Disease associations (from GenCC):

MPI-congenital disorder of glycosylation
Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Myriad Women’s Health, G2P, Orphanet, PanelApp Australia

MPI links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00872612).

BP6

Variant 15-74890083-C-T is Benign according to our data. Variant chr15-74890083-C-T is described in ClinVar as Conflicting_classifications_of_pathogenicity. ClinVar VariationId is 282926.

BS1

Variant frequency is greater than expected in population amr. GnomAd4 allele frequency = 0.00139 (211/152320) while in subpopulation AMR AF = 0.00314 (48/15302). AF 95% confidence interval is 0.00243. There are 1 homozygotes in GnomAd4. There are 98 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.

BS2

High Homozygotes in GnomAdExome4 at 12 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002435.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MPI	NM_002435.3	MANE Select	c.10C>T	p.Pro4Ser	missense	Exon 1 of 8	NP_002426.1	P34949-1
MPI	NM_001289157.2		c.10C>T	p.Pro4Ser	missense	Exon 1 of 7	NP_001276086.1	P34949-2
MPI	NM_001289155.2		c.10C>T	p.Pro4Ser	missense	Exon 1 of 7	NP_001276084.1	H3BPP3

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MPI	ENST00000352410.9	TSL:1 MANE Select	c.10C>T	p.Pro4Ser	missense	Exon 1 of 8	ENSP00000318318.6	P34949-1
MPI	ENST00000323744.10	TSL:1	c.10C>T	p.Pro4Ser	missense	Exon 1 of 7	ENSP00000318192.6	P34949-2
MPI	ENST00000563422.5	TSL:1	c.10C>T	p.Pro4Ser	missense	Exon 1 of 6	ENSP00000457885.1	H3BUZ9

Frequencies

GnomAD3 genomes

AF:

0.00139

AC:

212

AN:

152202

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000362

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00314

Gnomad ASJ

AF:

0.0130

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00118

Gnomad OTH

AF:

0.00622

GnomAD2 exomes

AF:

0.00192

AC:

471

AN:

245092

AF XY:

0.00193

show subpopulations

Gnomad AFR exome

AF:

0.000248

Gnomad AMR exome

AF:

0.00351

Gnomad ASJ exome

AF:

0.0102

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00156

Gnomad OTH exome

AF:

0.00462

GnomAD4 exome

AF:

0.00141

AC:

2051

AN:

1455616

Hom.:

Cov.:

AF XY:

0.00147

AC XY:

1066

AN XY:

724490

show subpopulations

African (AFR)

AF:

0.000717

AC:

AN:

33466

American (AMR)

AF:

0.00333

AC:

149

AN:

44714

Ashkenazi Jewish (ASJ)

AF:

0.0112

AC:

292

AN:

26122

East Asian (EAS)

AF:

0.0000252

AC:

AN:

39696

South Asian (SAS)

AF:

0.00123

AC:

106

AN:

86238

European-Finnish (FIN)

AF:

0.00

AC:

AN:

47482

Middle Eastern (MID)

AF:

0.0235

AC:

132

AN:

5628

European-Non Finnish (NFE)

AF:

0.00105

AC:

1169

AN:

1111938

Other (OTH)

AF:

0.00295

AC:

178

AN:

60332

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

121

243

364

486

607

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

132

176

220

<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:

0.00139

AC:

211

AN:

152320

Hom.:

Cov.:

AF XY:

0.00132

AC XY:

AN XY:

74480

show subpopulations

African (AFR)

AF:

0.000361

AC:

AN:

41588

American (AMR)

AF:

0.00314

AC:

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0130

AC:

AN:

3472

East Asian (EAS)

AF:

0.00

AC:

AN:

5162

South Asian (SAS)

AF:

0.000622

AC:

AN:

4826

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10620

Middle Eastern (MID)

AF:

0.0238

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00116

AC:

AN:

68034

Other (OTH)

AF:

0.00663

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.491

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.00190

Hom.:

Bravo

AF:

0.00182

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.000259

AC:

ESP6500AA

AF:

0.000228

AC:

ESP6500EA

AF:

0.00186

AC:

ExAC

AF:

0.00163

AC:

198

Asia WGS

AF:

0.000866

AC:

AN:

3478

EpiCase

AF:

0.00289

EpiControl

AF:

0.00243

ClinVar

ClinVar submissions as Germline

Significance:Conflicting classifications of pathogenicity

Revision:criteria provided, conflicting classifications

View on ClinVar

Pathogenic

VUS

Benign

Condition

MPI-congenital disorder of glycosylation (5)

not provided (5)

MPI-related disorder (1)

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.18

BayesDel_noAF

Uncertain

-0.030

CADD

Benign

(source)

DANN

Benign

0.72

DEOGEN2

Benign

0.33

Eigen

Benign

-0.78

Eigen_PC

Benign

-0.84

FATHMM_MKL

Benign

0.15

LIST_S2

Uncertain

0.86

M_CAP

Uncertain

0.10

MetaRNN

Benign

0.0087

MetaSVM

Uncertain

0.098

MutationAssessor

Benign

0.99

PhyloP100

1.2

PrimateAI

Benign

0.36

PROVEAN

Benign

0.21

REVEL

Uncertain

0.40

Sift

Benign

0.34

Sift4G

Benign

0.69

Polyphen

0.0020

Vest4

0.17

MVP

0.75

MPC

0.19

ClinPred

0.0060

GERP RS

2.0

PromoterAI

-0.044

Neutral

(source)

Varity_R

0.029

gMVP

0.24

Mutation Taster

=297/3

polymorphism

(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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over