Genetic Variant NM_014994.3:c.207-150_207-144dupAAAAAAA (chr15-41810717-C-CAAAAAAA) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_014994.3(MAPKBP1):c.207-150_207-144dupAAAAAAA variant causes a intron 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 0.0 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0000058 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MAPKBP1
NM_014994.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.616

Publications

0 publications found

Variant links:

Genes affected

MAPKBP1 (HGNC:29536): (mitogen-activated protein kinase binding protein 1) This gene encodes a scaffold protein that regulates the JNK (c-Jun N-terminal kinase) and NOD2 (nucleotide-binding oligomerization domain-containing protein 2) signaling pathways. The encoded protein interacts with another related JNK pathway scaffold protein, WDR62, via a conserved dimerization domain, and enhances JNK signaling. This protein may play a role in bacterial immunity by binding to the NOD2 receptor and negatively regulating downstream antibacterial and pro-inflammatory signaling. Mutations in this gene that impair cellular localization of the encoded protein cause a form of nephronophthisis, an autosomal-recessive kidney disorder, in human patients. [provided by RefSeq, May 2017]

MAPKBP1 Gene-Disease associations (from GenCC):

nephronophthisis 20
Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), ClinGen
late-onset nephronophthisis
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
nephronophthisis 1
Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

MAPKBP1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014994.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAPKBP1	NM_014994.3	MANE Select	c.207-150_207-144dupAAAAAAA	intron	N/A	NP_055809.2	O60336-6
MAPKBP1	NM_001128608.2		c.207-150_207-144dupAAAAAAA	intron	N/A	NP_001122080.1	O60336-1
MAPKBP1	NM_001265611.2		c.207-150_207-144dupAAAAAAA	intron	N/A	NP_001252540.1	O60336-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
MAPKBP1	ENST00000457542.7	TSL:1 MANE Select	c.207-150_207-144dupAAAAAAA	intron	N/A	ENSP00000397570.2	O60336-6
MAPKBP1	ENST00000456763.6	TSL:1	c.207-150_207-144dupAAAAAAA	intron	N/A	ENSP00000393099.2	O60336-1
MAPKBP1	ENST00000514566.5	TSL:1	c.207-150_207-144dupAAAAAAA	intron	N/A	ENSP00000426154.1	O60336-2

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

84082

Hom.:

Cov.:

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.00000575

AC:

AN:

347806

Hom.:

Cov.:

AF XY:

0.0000109

AC XY:

AN XY:

183564

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

9926

American (AMR)

AF:

0.00

AC:

AN:

13540

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10422

East Asian (EAS)

AF:

0.00

AC:

AN:

22104

South Asian (SAS)

AF:

0.00

AC:

AN:

35886

European-Finnish (FIN)

AF:

0.0000783

AC:

AN:

25554

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1506

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

209030

Other (OTH)

AF:

0.00

AC:

AN:

19838

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.450

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

84082

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

38868

African (AFR)

AF:

0.00

AC:

AN:

23272

American (AMR)

AF:

0.00

AC:

AN:

7712

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2218

East Asian (EAS)

AF:

0.00

AC:

AN:

2692

South Asian (SAS)

AF:

0.00

AC:

AN:

2396

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2628

Middle Eastern (MID)

AF:

0.00

AC:

AN:

174

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

41364

Other (OTH)

AF:

0.00

AC:

AN:

1096

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.62

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

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