NM_001364716.4:c.563_568dupGCAGCA

Variant names:

• chr17-17136247-C-CCAGCAG
• rs3833098
• NM_001364716.4:c.563_568dupGCAGCA

Variant summary

Our verdict is Likely benign. Variant got -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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

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]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• BP3: Nonframeshift variant in repetitive region in NM_001364716.4

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
MPRIP	NM_001364716.4	c.563_568dupGCAGCA	p.Ser188_Ser189dup	disruptive_inframe_insertion	Exon 6 of 24	ENST00000651222.2	NP_001351645.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
MPRIP	ENST00000651222.2	c.563_568dupGCAGCA	p.Ser188_Ser189dup	disruptive_inframe_insertion	Exon 6 of 24		NM_001364716.4	ENSP00000498253.1

Frequencies

GnomAD3 genomes AF: 0.000213 AC: 32 AN: 150558 Hom.: 0 Cov.: 0

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.: 0 Cov.: 0 AF XY: 0.000106 AC XY: 74 AN XY: 699204

Gnomad4 AFR exome AF: 0.000620

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.000952

Gnomad4 EAS exome AF: 0.0000802

Gnomad4 SAS exome AF: 0.0000844

Gnomad4 FIN exome AF: 0.000121

Gnomad4 NFE exome AF: 0.0000718

Gnomad4 OTH exome AF: 0.000138

GnomAD4 genome AF: 0.000212 AC: 32 AN: 150672 Hom.: 0 Cov.: 0 AF XY: 0.000258 AC XY: 19 AN XY: 73550

Gnomad4 AFR AF: 0.000464

Gnomad4 AMR AF: 0.000132

Gnomad4 ASJ AF: 0.000289

Gnomad4 EAS AF: 0.000394

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000118

Gnomad4 OTH AF: 0.00

Bravo AF: 0.000227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3833098; hg19: chr17-17039561;