1-213996713-C-A
Variant names:
Variant summary
Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2
The NM_001270616.2(PROX1):c.178C>A(p.Gln60Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q60E) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 32)
Consequence
PROX1
NM_001270616.2 missense
NM_001270616.2 missense
Scores
2
6
11
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 7.50
Publications
0 publications found
Genes affected
PROX1 (HGNC:9459): (prospero homeobox 1) The protein encoded by this gene is a member of the homeobox transcription factor family. Members of this family contain a homeobox domain that consists of a 60-amino acid helix-turn-helix structure that binds DNA and RNA. The protein encoded by this gene is conserved across vertebrates and may play an essential role during development. Altered levels of this protein have been reported in cancers of different organs, such as colon, brain, blood, breast, pancreas, liver and esophagus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2012]
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ACMG classification
Classification was made for transcript
Our verdict: Uncertain_significance. The variant received 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| PROX1 | ENST00000366958.9 | c.178C>A | p.Gln60Lys | missense_variant | Exon 2 of 5 | 1 | NM_001270616.2 | ENSP00000355925.4 | ||
| PROX1 | ENST00000435016.2 | c.178C>A | p.Gln60Lys | missense_variant | Exon 2 of 5 | 1 | ENSP00000400694.1 | |||
| PROX1 | ENST00000471129.1 | c.178C>A | p.Gln60Lys | missense_variant | Exon 2 of 2 | 3 | ENSP00000419517.1 | |||
| PROX1 | ENST00000607425.1 | c.178C>A | p.Gln60Lys | missense_variant | Exon 2 of 2 | 3 | ENSP00000475357.1 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251474 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
1
AN:
251474
AF XY:
Gnomad AFR exome
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Gnomad AMR exome
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Gnomad ASJ exome
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Gnomad EAS exome
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Gnomad FIN exome
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GnomAD4 exome Cov.: 31
GnomAD4 exome
Cov.:
31
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
DANN
Uncertain
DEOGEN2
Benign
.;T;T;T;T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;.;.;D;.;D
M_CAP
Benign
T
MetaRNN
Uncertain
D;D;D;D;D;D
MetaSVM
Benign
T
MutationAssessor
Benign
.;L;L;L;L;.
PhyloP100
PrimateAI
Pathogenic
D
PROVEAN
Benign
N;N;N;N;N;.
REVEL
Benign
Sift
Benign
T;D;T;D;D;.
Sift4G
Benign
T;T;T;T;T;T
Polyphen
0.22
.;B;B;B;B;.
Vest4
0.76, 0.75, 0.76, 0.76
MutPred
Gain of ubiquitination at Q60 (P = 0.0082);Gain of ubiquitination at Q60 (P = 0.0082);Gain of ubiquitination at Q60 (P = 0.0082);Gain of ubiquitination at Q60 (P = 0.0082);Gain of ubiquitination at Q60 (P = 0.0082);Gain of ubiquitination at Q60 (P = 0.0082);
MVP
MPC
1.0
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
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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