11-24914534-T-A
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Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001009909.4(LUZP2):c.518T>A(p.Phe173Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.00000998 in 1,603,282 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000059 ( 0 hom., cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
LUZP2
NM_001009909.4 missense
NM_001009909.4 missense
Scores
3
16
Clinical Significance
Conservation
PhyloP100: 4.41
Genes affected
LUZP2 (HGNC:23206): (leucine zipper protein 2) This gene encodes a leucine zipper protein. This protein is deleted in some patients with Wilms tumor-Aniridia-Genitourinary anomalies-mental Retardation (WAGR) syndrome. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Oct 2011]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.17896333).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LUZP2 | NM_001009909.4 | c.518T>A | p.Phe173Tyr | missense_variant | 7/12 | ENST00000336930.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LUZP2 | ENST00000336930.11 | c.518T>A | p.Phe173Tyr | missense_variant | 7/12 | 1 | NM_001009909.4 | P1 | |
LUZP2 | ENST00000533227.5 | c.260T>A | p.Phe87Tyr | missense_variant | 7/12 | 1 | |||
LUZP2 | ENST00000620308.1 | c.260T>A | p.Phe87Tyr | missense_variant | 6/11 | 5 | |||
LUZP2 | ENST00000529015.5 | c.397-62057T>A | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152176Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.00000827 AC: 2AN: 241790Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 131024
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GnomAD4 exome AF: 0.00000482 AC: 7AN: 1450988Hom.: 0 Cov.: 28 AF XY: 0.00000416 AC XY: 3AN XY: 721984
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GnomAD4 genome AF: 0.0000591 AC: 9AN: 152294Hom.: 0 Cov.: 32 AF XY: 0.0000537 AC XY: 4AN XY: 74464
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 17, 2023 | The c.518T>A (p.F173Y) alteration is located in exon 7 (coding exon 7) of the LUZP2 gene. This alteration results from a T to A substitution at nucleotide position 518, causing the phenylalanine (F) at amino acid position 173 to be replaced by a tyrosine (Y). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.;T
M_CAP
Benign
T
MetaRNN
Benign
T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;.;.
MutationTaster
Benign
N;N
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;.
REVEL
Benign
Sift
Benign
D;D;.
Sift4G
Benign
T;T;T
Polyphen
P;.;.
Vest4
MutPred
Loss of methylation at K174 (P = 0.0339);.;.;
MVP
MPC
ClinPred
T
GERP RS
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gMVP
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