12-76849415-G-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_015336.4(ZDHHC17):c.1705G>T(p.Ala569Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000214 in 1,401,870 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000021 ( 0 hom. )
Consequence
ZDHHC17
NM_015336.4 missense
NM_015336.4 missense
Scores
4
5
10
Clinical Significance
Conservation
PhyloP100: 9.96
Genes affected
ZDHHC17 (HGNC:18412): (zinc finger DHHC-type palmitoyltransferase 17) Enables identical protein binding activity and protein-cysteine S-palmitoyltransferase activity. Involved in lipoprotein transport and protein palmitoylation. Located in Golgi membrane; Golgi-associated vesicle membrane; and aggresome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ZDHHC17 | NM_015336.4 | c.1705G>T | p.Ala569Ser | missense_variant | 16/17 | ENST00000426126.7 | |
ZDHHC17 | NM_001359626.1 | c.1675G>T | p.Ala559Ser | missense_variant | 16/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ZDHHC17 | ENST00000426126.7 | c.1705G>T | p.Ala569Ser | missense_variant | 16/17 | 1 | NM_015336.4 | P1 | |
ZDHHC17 | ENST00000547673.1 | n.193G>T | non_coding_transcript_exon_variant | 2/2 | 2 | ||||
ZDHHC17 | ENST00000550244.1 | n.587G>T | non_coding_transcript_exon_variant | 3/4 | 3 | ||||
ZDHHC17 | ENST00000553091.5 | n.449G>T | non_coding_transcript_exon_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD4 exome AF: 0.00000214 AC: 3AN: 1401870Hom.: 0 Cov.: 29 AF XY: 0.00000433 AC XY: 3AN XY: 692836
GnomAD4 exome
AF:
AC:
3
AN:
1401870
Hom.:
Cov.:
29
AF XY:
AC XY:
3
AN XY:
692836
Gnomad4 AFR exome
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GnomAD4 genome Cov.: 32
GnomAD4 genome
Cov.:
32
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 | May 03, 2023 | The c.1705G>T (p.A569S) alteration is located in exon 16 (coding exon 16) of the ZDHHC17 gene. This alteration results from a G to T substitution at nucleotide position 1705, causing the alanine (A) at amino acid position 569 to be replaced by a serine (S). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Benign
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D
M_CAP
Benign
T
MetaRNN
Uncertain
D
MetaSVM
Benign
T
MutationAssessor
Benign
L
MutationTaster
Benign
D;D
PrimateAI
Pathogenic
D
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Polyphen
D
Vest4
MutPred
Gain of disorder (P = 0.0176);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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
No publications associated with this variant yet.