rs761991070
Positions:
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PP3_ModeratePP5BS2
The NM_002461.3(MVD):āc.746T>Cā(p.Phe249Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000218 in 1,602,610 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 Pathogenic (no stars).
Frequency
Genomes: š 0.000020 ( 0 hom., cov: 34)
Exomes š: 0.000022 ( 0 hom. )
Consequence
MVD
NM_002461.3 missense
NM_002461.3 missense
Scores
8
10
1
Clinical Significance
Conservation
PhyloP100: 6.65
Genes affected
MVD (HGNC:7529): (mevalonate diphosphate decarboxylase) The enzyme mevalonate pyrophosphate decarboxylase catalyzes the conversion of mevalonate pyrophosphate into isopentenyl pyrophosphate in one of the early steps in cholesterol biosynthesis. It decarboxylates and dehydrates its substrate while hydrolyzing ATP. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -1 ACMG points.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.93
PP5
?
Variant 16-88655350-A-G is Pathogenic according to our data. Variant chr16-88655350-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 253039.Status of the report is no_assertion_criteria_provided, 0 stars.
BS2
?
High AC in GnomAdExome4 at 32 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MVD | NM_002461.3 | c.746T>C | p.Phe249Ser | missense_variant | 7/10 | ENST00000301012.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MVD | ENST00000301012.8 | c.746T>C | p.Phe249Ser | missense_variant | 7/10 | 1 | NM_002461.3 | P1 | |
MVD | ENST00000565149.5 | n.1305T>C | non_coding_transcript_exon_variant | 3/6 | 1 | ||||
MVD | ENST00000569177.5 | downstream_gene_variant | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 34
GnomAD3 genomes
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GnomAD3 exomes AF: 0.0000482 AC: 11AN: 227992Hom.: 0 AF XY: 0.0000405 AC XY: 5AN XY: 123532
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GnomAD4 exome AF: 0.0000221 AC: 32AN: 1450398Hom.: 0 Cov.: 32 AF XY: 0.0000222 AC XY: 16AN XY: 720478
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152212Hom.: 0 Cov.: 34 AF XY: 0.0000269 AC XY: 2AN XY: 74360
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ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
Porokeratosis 7, multiple types Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 23, 2015 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Pathogenic
D
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D
M_CAP
Uncertain
D
MetaRNN
Pathogenic
D
MetaSVM
Uncertain
D
MutationAssessor
Pathogenic
H
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D
REVEL
Uncertain
Sift
Pathogenic
D
Sift4G
Pathogenic
D
Polyphen
D
Vest4
MutPred
Gain of disorder (P = 0.0039);
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
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