GeneBe

rs58612719

Variant names:

Variant summary

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

The NM_014994.3(MAPKBP1):​c.207-159_207-144delAAAAAAAAAAAAAAAA variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000288 in 347,806 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 0)
Exomes 𝑓: 0.0000029 ( 0 hom. )

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

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

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MAPKBP1
NM_014994.3
MANE Select
c.207-159_207-144delAAAAAAAAAAAAAAAA
intron
N/ANP_055809.2O60336-6
MAPKBP1
NM_001128608.2
c.207-159_207-144delAAAAAAAAAAAAAAAA
intron
N/ANP_001122080.1O60336-1
MAPKBP1
NM_001265611.2
c.207-159_207-144delAAAAAAAAAAAAAAAA
intron
N/ANP_001252540.1O60336-2

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
MAPKBP1
ENST00000457542.7
TSL:1 MANE Select
c.207-159_207-144delAAAAAAAAAAAAAAAA
intron
N/AENSP00000397570.2O60336-6
MAPKBP1
ENST00000456763.6
TSL:1
c.207-159_207-144delAAAAAAAAAAAAAAAA
intron
N/AENSP00000393099.2O60336-1
MAPKBP1
ENST00000514566.5
TSL:1
c.207-159_207-144delAAAAAAAAAAAAAAAA
intron
N/AENSP00000426154.1O60336-2

Frequencies

GnomAD3 genomes
Cov.:
0
GnomAD4 exome
AF:
0.00000288
AC:
1
AN:
347806
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
183564
show subpopulations
African (AFR)
AF:
0.00
AC:
0
AN:
9926
American (AMR)
AF:
0.00
AC:
0
AN:
13540
Ashkenazi Jewish (ASJ)
AF:
0.00
AC:
0
AN:
10422
East Asian (EAS)
AF:
0.00
AC:
0
AN:
22104
South Asian (SAS)
AF:
0.0000279
AC:
1
AN:
35886
European-Finnish (FIN)
AF:
0.00
AC:
0
AN:
25554
Middle Eastern (MID)
AF:
0.00
AC:
0
AN:
1506
European-Non Finnish (NFE)
AF:
0.00
AC:
0
AN:
209030
Other (OTH)
AF:
0.00
AC:
0
AN:
19838
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.675
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Exome Het
Variant carriers
0
2
4
6
8
10
<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
Cov.:
0

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

Other links and lift over

dbSNP: rs58612719; hg19: chr15-42102915; API