17-6451873-ACCC-ACCCCCCC
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_031220.4(PITPNM3):c.*3461_*3464dupGGGG 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 0.0092 ( 117 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
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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 0.00921 AC: 404AN: 43866Hom.: 117 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
404
AN:
43866
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 0.00921 AC: 404AN: 43880Hom.: 117 Cov.: 0 AF XY: 0.00799 AC XY: 162AN XY: 20278 show subpopulations
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
AF:
AC:
404
AN:
43880
Hom.:
Cov.:
0
AF XY:
AC XY:
162
AN XY:
20278
show subpopulations
African (AFR)
AF:
AC:
142
AN:
11846
American (AMR)
AF:
AC:
19
AN:
3618
Ashkenazi Jewish (ASJ)
AF:
AC:
4
AN:
1308
East Asian (EAS)
AF:
AC:
20
AN:
1392
South Asian (SAS)
AF:
AC:
2
AN:
982
European-Finnish (FIN)
AF:
AC:
13
AN:
2100
Middle Eastern (MID)
AF:
AC:
1
AN:
74
European-Non Finnish (NFE)
AF:
AC:
187
AN:
21636
Other (OTH)
AF:
AC:
3
AN:
526
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.470
Heterozygous variant carriers
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Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
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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
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