Genetic Variant MPRIP:p.Ser188_Ser189dup (chr17-17136247-C-CCAGCAG) – ACMG Classification: Likely_benign (-1 pts)

Variant summary

Our verdict is Likely benign. The variant received -1 ACMG points: 0P and 1B. BP3

The NM_001364716.4(MPRIP):c.563_568dupGCAGCA(p.Ser188_Ser189dup) variant causes a disruptive inframe insertion change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.00021 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00010 ( 0 hom. )

Consequence

MPRIP
NM_001364716.4 disruptive_inframe_insertion

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.511

Publications

15 publications found

Variant links:

Genes affected

MPRIP (HGNC:30321): (myosin phosphatase Rho interacting protein) Enables cadherin binding activity. Predicted to be involved in actin filament organization. Located in actin cytoskeleton and cytosol. [provided by Alliance of Genome Resources, Apr 2022]

MPRIP links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -1 ACMG points.

BP3

Nonframeshift variant in repetitive region in NM_001364716.4

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001364716.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MPRIP	NM_001364716.4	MANE Select	c.563_568dupGCAGCA	p.Ser188_Ser189dup	disruptive_inframe_insertion	Exon 6 of 24	NP_001351645.2	A0A494BZV2
MPRIP	NM_015134.4		c.563_568dupGCAGCA	p.Ser188_Ser189dup	disruptive_inframe_insertion	Exon 6 of 23	NP_055949.2	Q6WCQ1-2
MPRIP	NM_201274.4		c.563_568dupGCAGCA	p.Ser188_Ser189dup	disruptive_inframe_insertion	Exon 6 of 24	NP_958431.2	Q6WCQ1-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
MPRIP	ENST00000651222.2	MANE Select	c.563_568dupGCAGCA	p.Ser188_Ser189dup	disruptive_inframe_insertion	Exon 6 of 24	ENSP00000498253.1	A0A494BZV2
MPRIP	ENST00000395811.9	TSL:1	c.563_568dupGCAGCA	p.Ser188_Ser189dup	disruptive_inframe_insertion	Exon 6 of 23	ENSP00000379156.4	Q6WCQ1-2
MPRIP	ENST00000584067.5	TSL:1	c.95_100dupGCAGCA	p.Ser32_Ser33dup	disruptive_inframe_insertion	Exon 2 of 18	ENSP00000462688.1	J3KSW8

Frequencies

GnomAD3 genomes

AF:

0.000213

AC:

AN:

150558

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000465

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000132

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.000393

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000118

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.000103

AC:

145

AN:

1405352

Hom.:

Cov.:

AF XY:

0.000106

AC XY:

AN XY:

699204

show subpopulations

African (AFR)

AF:

0.000620

AC:

AN:

32276

American (AMR)

AF:

0.00

AC:

AN:

42486

Ashkenazi Jewish (ASJ)

AF:

0.000952

AC:

AN:

25202

East Asian (EAS)

AF:

0.0000802

AC:

AN:

37396

South Asian (SAS)

AF:

0.0000844

AC:

AN:

82924

European-Finnish (FIN)

AF:

0.000121

AC:

AN:

49608

Middle Eastern (MID)

AF:

0.00

AC:

AN:

5640

European-Non Finnish (NFE)

AF:

0.0000718

AC:

AN:

1071916

Other (OTH)

AF:

0.000138

AC:

AN:

57904

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.451

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome 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

GnomAD4 genome

AF:

0.000212

AC:

AN:

150672

Hom.:

Cov.:

AF XY:

0.000258

AC XY:

AN XY:

73550

show subpopulations

African (AFR)

AF:

0.000464

AC:

AN:

40966

American (AMR)

AF:

0.000132

AC:

AN:

15122

Ashkenazi Jewish (ASJ)

AF:

0.000289

AC:

AN:

3464

East Asian (EAS)

AF:

0.000394

AC:

AN:

5078

South Asian (SAS)

AF:

0.00

AC:

AN:

4728

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10400

Middle Eastern (MID)

AF:

0.00

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.000118

AC:

AN:

67626

Other (OTH)

AF:

0.00

AC:

AN:

2088

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.506

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:

0.000416

Hom.:

3215

Bravo

AF:

0.000227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

-0.51

Mutation Taster

=76/24

polymorphism

(source)

Splicing

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