rs555349004
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Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The ENST00000327532.7(DZIP1L):c.269C>T(p.Ala90Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000205 in 1,612,688 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: 𝑓 0.000033 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000019 ( 0 hom. )
Consequence
DZIP1L
ENST00000327532.7 missense
ENST00000327532.7 missense
Scores
5
9
5
Clinical Significance
Conservation
PhyloP100: 7.23
Genes affected
DZIP1L (HGNC:26551): (DAZ interacting zinc finger protein 1 like) Predicted to enable metal ion binding activity. Involved in cilium assembly and regulation of protein localization. Located in ciliary basal body. Colocalizes with centriole. Implicated in polycystic kidney disease 5. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP5
Variant 3-138103703-G-A is Pathogenic according to our data. Variant chr3-138103703-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 431431.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
DZIP1L | NM_173543.3 | c.269C>T | p.Ala90Val | missense_variant | 2/16 | ENST00000327532.7 | NP_775814.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
DZIP1L | ENST00000327532.7 | c.269C>T | p.Ala90Val | missense_variant | 2/16 | 1 | NM_173543.3 | ENSP00000332148 | P2 | |
DZIP1L | ENST00000469243.5 | c.269C>T | p.Ala90Val | missense_variant | 3/14 | 2 | ENSP00000419486 | A2 | ||
DZIP1L | ENST00000490472.1 | n.76C>T | non_coding_transcript_exon_variant | 1/4 | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152206Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000361 AC: 9AN: 249264Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135034
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GnomAD4 exome AF: 0.0000192 AC: 28AN: 1460364Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 726560
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GnomAD4 genome AF: 0.0000328 AC: 5AN: 152324Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74494
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Polycystic kidney disease 5 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 07, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M
MutationTaster
Benign
D;D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MutPred
Gain of ubiquitination at K85 (P = 0.0638);Gain of ubiquitination at K85 (P = 0.0638);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
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