6-46550418-C-T
Position:
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_016593.5(CYP39A1):c.1358G>A(p.Gly453Asp) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,459,412 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000014 ( 0 hom. )
Consequence
CYP39A1
NM_016593.5 missense
NM_016593.5 missense
Scores
9
8
2
Clinical Significance
Conservation
PhyloP100: 3.84
Genes affected
CYP39A1 (HGNC:17449): (cytochrome P450 family 39 subfamily A member 1) This gene encodes a member of the cytochrome P450 superfamily of enzymes. The cytochrome P450 proteins are monooxygenases which catalyze many reactions involved in drug metabolism and synthesis of cholesterol, steroids and other lipids. This endoplasmic reticulum protein is involved in the conversion of cholesterol to bile acids. Its substrates include the oxysterols 25-hydroxycholesterol, 27-hydroxycholesterol and 24-hydroxycholesterol. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP3
MetaRNN computational evidence supports a deleterious effect, 0.857
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP39A1 | NM_016593.5 | c.1358G>A | p.Gly453Asp | missense_variant | 12/12 | ENST00000275016.3 | |
CYP39A1 | NM_001278738.2 | c.1298G>A | p.Gly433Asp | missense_variant | 12/12 | ||
CYP39A1 | NM_001278739.2 | c.842G>A | p.Gly281Asp | missense_variant | 11/11 | ||
CYP39A1 | XM_017010924.2 | c.1250G>A | p.Gly417Asp | missense_variant | 11/11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP39A1 | ENST00000275016.3 | c.1358G>A | p.Gly453Asp | missense_variant | 12/12 | 1 | NM_016593.5 | P1 | |
CYP39A1 | ENST00000619708.4 | c.842G>A | p.Gly281Asp | missense_variant | 11/11 | 1 | |||
RCAN2-DT | ENST00000657801.1 | n.286+17903C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000805 AC: 2AN: 248360Hom.: 0 AF XY: 0.00000745 AC XY: 1AN XY: 134214
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GnomAD4 exome AF: 0.00000137 AC: 2AN: 1459412Hom.: 0 Cov.: 30 AF XY: 0.00000138 AC XY: 1AN XY: 725930
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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 | Oct 12, 2022 | The c.1358G>A (p.G453D) alteration is located in exon 12 (coding exon 12) of the CYP39A1 gene. This alteration results from a G to A substitution at nucleotide position 1358, causing the glycine (G) at amino acid position 453 to be replaced by an aspartic acid (D). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Benign
.;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
.;M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
.;D
REVEL
Uncertain
Sift
Pathogenic
.;D
Sift4G
Pathogenic
D;D
Polyphen
1.0
.;D
Vest4
MutPred
0.66
.;Gain of relative solvent accessibility (P = 0.09);
MVP
MPC
0.31
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