rs879195140
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_031220.4(PITPNM3):c.*3453_*3454insT 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 0.000013 ( 0 hom., cov: 0)
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: 0.00
Publications
1 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 0.0000127 AC: 1AN: 78560Hom.: 0 Cov.: 0 show subpopulations
GnomAD3 genomes
AF:
AC:
1
AN:
78560
Hom.:
Cov.:
0
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GnomAD4 exome Cov.: 0
GnomAD4 exome
Cov.:
0
GnomAD4 genome 0.0000127 AC: 1AN: 78614Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 38342 show subpopulations ⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
GnomAD4 genome
AF:
AC:
1
AN:
78614
Hom.:
Cov.:
0
AF XY:
AC XY:
0
AN XY:
38342
show subpopulations
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.
African (AFR)
AF:
AC:
0
AN:
16824
American (AMR)
AF:
AC:
0
AN:
7340
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
1920
East Asian (EAS)
AF:
AC:
0
AN:
3738
South Asian (SAS)
AF:
AC:
0
AN:
2838
European-Finnish (FIN)
AF:
AC:
0
AN:
5796
Middle Eastern (MID)
AF:
AC:
0
AN:
174
European-Non Finnish (NFE)
AF:
AC:
1
AN:
38490
Other (OTH)
AF:
AC:
0
AN:
1006
⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.325
Heterozygous variant carriers
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0.95
Allele balance
Alfa
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ClinVar
Not reported inComputational scores
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PhyloP100
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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