Genetic Variant MAPKBP1:c.207-154_207-144delAAAAAAAAAAA (chr15-41810717-CAAAAAAAAAAA-C) – 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.207-154_207-144delAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type DEL_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000024 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

MAPKBP1
NM_014994.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.625

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.207-154_207-144delAAAAAAAAAAA	intron	N/A	NP_055809.2	O60336-6
MAPKBP1	NM_001128608.2		c.207-154_207-144delAAAAAAAAAAA	intron	N/A	NP_001122080.1	O60336-1
MAPKBP1	NM_001265611.2		c.207-154_207-144delAAAAAAAAAAA	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.207-154_207-144delAAAAAAAAAAA	intron	N/A	ENSP00000397570.2	O60336-6
MAPKBP1	ENST00000456763.6	TSL:1	c.207-154_207-144delAAAAAAAAAAA	intron	N/A	ENSP00000393099.2	O60336-1
MAPKBP1	ENST00000514566.5	TSL:1	c.207-154_207-144delAAAAAAAAAAA	intron	N/A	ENSP00000426154.1	O60336-2

Frequencies

GnomAD3 genomes

AF:

0.0000238

AC:

AN:

84084

Hom.:

Cov.:

show subpopulations

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:

0.0000484

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

347806

Hom.:

AF XY:

0.00

AC XY:

AN XY:

183564

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:

0.00

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

GnomAD4 genome

AF:

0.0000238

AC:

AN:

84084

Hom.:

Cov.:

AF XY:

0.0000515

AC XY:

AN XY:

38870

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

23272

American (AMR)

AF:

0.00

AC:

AN:

7712

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2220

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:

0.0000484

AC:

AN:

41364

Other (OTH)

AF:

0.00

AC:

AN:

1096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.650

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:

0.00

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.63

Splicing

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

Publications

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15-41810717-CAAAAAAAAAAAAAAAA-CAAAAA

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over