17-6451873-ACCC-ACCCCCC
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_031220.4(PITPNM3):c.*3462_*3464dupGGG variant causes a 3 prime UTR 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 0.036 ( 394 hom., cov: 0)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
PITPNM3
NM_031220.4 3_prime_UTR
NM_031220.4 3_prime_UTR
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.916
Publications
0 publications found
Genes affected
PITPNM3 (HGNC:21043): (PITPNM family member 3) This gene encodes a member of a family of membrane-associated phosphatidylinositol transfer domain-containing proteins. The calcium-binding protein has phosphatidylinositol (PI) transfer activity and interacts with the protein tyrosine kinase PTK2B (also known as PYK2). The protein is homologous to a Drosophila protein that is implicated in the visual transduction pathway in flies. Mutations in this gene result in autosomal dominant cone dystrophy. Multiple transcript variants encoding different isoforms have been found for this gene.[provided by RefSeq, Sep 2009]
PITPNM3 Gene-Disease associations (from GenCC):
- cone-rod dystrophy 5Inheritance: AD Classification: STRONG, LIMITED Submitted by: G2P, Labcorp Genetics (formerly Invitae)
- cone-rod dystrophyInheritance: AD 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_031220.4. You can select a different transcript below to see updated ACMG assignments.
Frequencies
GnomAD3 genomes 0.0358 AC: 1568AN: 43774Hom.: 394 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1568
AN:
43774
Hom.:
Cov.:
0
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 12Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 6
GnomAD4 exome
Data not reliable, filtered out with message: AC0;AS_VQSR
AF:
AC:
0
AN:
12
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
6
African (AFR)
AC:
0
AN:
0
American (AMR)
AC:
0
AN:
0
Ashkenazi Jewish (ASJ)
AC:
0
AN:
0
East Asian (EAS)
AC:
0
AN:
0
South Asian (SAS)
AC:
0
AN:
0
European-Finnish (FIN)
AC:
0
AN:
0
Middle Eastern (MID)
AC:
0
AN:
0
European-Non Finnish (NFE)
AF:
AC:
0
AN:
12
Other (OTH)
AC:
0
AN:
0
GnomAD4 genome 0.0358 AC: 1568AN: 43788Hom.: 394 Cov.: 0 AF XY: 0.0297 AC XY: 602AN XY: 20240 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
1568
AN:
43788
Hom.:
Cov.:
0
AF XY:
AC XY:
602
AN XY:
20240
show subpopulations
African (AFR)
AF:
AC:
321
AN:
11816
American (AMR)
AF:
AC:
111
AN:
3598
Ashkenazi Jewish (ASJ)
AF:
AC:
44
AN:
1310
East Asian (EAS)
AF:
AC:
79
AN:
1398
South Asian (SAS)
AF:
AC:
14
AN:
976
European-Finnish (FIN)
AF:
AC:
36
AN:
2088
Middle Eastern (MID)
AF:
AC:
2
AN:
74
European-Non Finnish (NFE)
AF:
AC:
920
AN:
21604
Other (OTH)
AF:
AC:
11
AN:
526
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
21
42
62
83
104
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
20
40
60
80
100
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.