chr14-56801588-C-G
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021728.4(OTX2):c.*147G>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000139 in 719,634 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
OTX2
NM_021728.4 3_prime_UTR
NM_021728.4 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.749
Publications
0 publications found
Genes affected
OTX2 (HGNC:8522): (orthodenticle homeobox 2) This gene encodes a member of the bicoid subfamily of homeodomain-containing transcription factors. The encoded protein acts as a transcription factor and plays a role in brain, craniofacial, and sensory organ development. The encoded protein also influences the proliferation and differentiation of dopaminergic neuronal progenitor cells during mitosis. Mutations in this gene cause syndromic microphthalmia 5 (MCOPS5) and combined pituitary hormone deficiency 6 (CPHD6). This gene is also suspected of having an oncogenic role in medulloblastoma. Alternative splicing results in multiple transcript variants encoding distinct isoforms. Pseudogenes of this gene are known to exist on chromosomes two and nine. [provided by RefSeq, Jul 2012]
OTX2 Gene-Disease associations (from GenCC):
- syndromic microphthalmia type 5Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: G2P, Labcorp Genetics (formerly Invitae), PanelApp Australia, Ambry Genetics, Orphanet
- pituitary hormone deficiency, combined, 6Inheritance: AD Classification: STRONG, MODERATE Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics
- combined pituitary hormone deficiencies, genetic formInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- isolated anophthalmia-microphthalmia syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- patterned macular dystrophyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- septooptic dysplasiaInheritance: 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.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.41).
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000139 AC: 1AN: 719634Hom.: 0 Cov.: 9 AF XY: 0.00000263 AC XY: 1AN XY: 379606 show subpopulations
GnomAD4 exome
AF:
AC:
1
AN:
719634
Hom.:
Cov.:
9
AF XY:
AC XY:
1
AN XY:
379606
show subpopulations
African (AFR)
AF:
AC:
0
AN:
18016
American (AMR)
AF:
AC:
1
AN:
33824
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
19766
East Asian (EAS)
AF:
AC:
0
AN:
34068
South Asian (SAS)
AF:
AC:
0
AN:
63708
European-Finnish (FIN)
AF:
AC:
0
AN:
41786
Middle Eastern (MID)
AF:
AC:
0
AN:
2654
European-Non Finnish (NFE)
AF:
AC:
0
AN:
470334
Other (OTH)
AF:
AC:
0
AN:
35478
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.525
Heterozygous variant carriers
0
0
1
1
2
2
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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