rs750473506

Positions:

Variant summary

Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP2PP3_ModeratePP5

The NM_001378452.1(ITPR1):ā€‹c.2683A>Gā€‹(p.Ile895Val) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000206 in 1,458,030 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 Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: not found (cov: 32)
Exomes š‘“: 0.0000021 ( 0 hom. )

Consequence

ITPR1
NM_001378452.1 missense

Scores

12
5
2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1U:2

Conservation

PhyloP100: 8.86
Variant links:
Genes affected
ITPR1 (HGNC:6180): (inositol 1,4,5-trisphosphate receptor type 1) This gene encodes an intracellular receptor for inositol 1,4,5-trisphosphate. Upon stimulation by inositol 1,4,5-trisphosphate, this receptor mediates calcium release from the endoplasmic reticulum. Mutations in this gene cause spinocerebellar ataxia type 15, a disease associated with an heterogeneous group of cerebellar disorders. Multiple transcript variants have been identified for this gene. [provided by RefSeq, Nov 2009]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_pathogenic. Variant got 6 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), ITPR1. . Gene score misZ 5.5951 (greater than the threshold 3.09). Trascript score misZ 6.2026 (greater than threshold 3.09). GenCC has associacion of gene with spinocerebellar ataxia type 15/16, aniridia-cerebellar ataxia-intellectual disability syndrome, spinocerebellar ataxia type 29.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.863
PP5
Variant 3-4675152-A-G is Pathogenic according to our data. Variant chr3-4675152-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 586044.We mark this variant Likely_pathogenic, oryginal submissions are: {Uncertain_significance=2, Likely_pathogenic=1}.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
ITPR1NM_001378452.1 linkuse as main transcriptc.2683A>G p.Ile895Val missense_variant 23/62 ENST00000649015.2 NP_001365381.1
ITPR1NM_001168272.2 linkuse as main transcriptc.2638A>G p.Ile880Val missense_variant 22/61 NP_001161744.1 Q14643-2
ITPR1NM_001099952.4 linkuse as main transcriptc.2683A>G p.Ile895Val missense_variant 23/59 NP_001093422.2 Q14643-3B4DER3Q59H91
ITPR1NM_002222.7 linkuse as main transcriptc.2638A>G p.Ile880Val missense_variant 22/58 NP_002213.5 Q14643-4B4DER3B4DGH1Q59H91

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
ITPR1ENST00000649015.2 linkuse as main transcriptc.2683A>G p.Ile895Val missense_variant 23/62 NM_001378452.1 ENSP00000497605.1 Q14643-1
ITPR1ENST00000354582.12 linkuse as main transcriptc.2683A>G p.Ile895Val missense_variant 23/625 ENSP00000346595.8 A0A3F2YNW8
ITPR1ENST00000648266.1 linkuse as main transcriptc.2683A>G p.Ile895Val missense_variant 23/62 ENSP00000498014.1 A0A3B3IU04
ITPR1ENST00000650294.1 linkuse as main transcriptc.2638A>G p.Ile880Val missense_variant 22/61 ENSP00000498056.1 A0A3B3ITU8
ITPR1ENST00000443694.5 linkuse as main transcriptc.2638A>G p.Ile880Val missense_variant 22/611 ENSP00000401671.2 Q14643-2
ITPR1ENST00000648309.1 linkuse as main transcriptc.2638A>G p.Ile880Val missense_variant 20/59 ENSP00000497026.1 Q14643-5
ITPR1ENST00000357086.10 linkuse as main transcriptc.2683A>G p.Ile895Val missense_variant 23/591 ENSP00000349597.4 Q14643-3
ITPR1ENST00000456211.8 linkuse as main transcriptc.2638A>G p.Ile880Val missense_variant 22/581 ENSP00000397885.2 Q14643-4
ITPR1ENST00000648038.1 linkuse as main transcriptc.520A>G p.Ile174Val missense_variant 4/42 ENSP00000497872.1 A0A3B3ITQ1
ITPR1ENST00000648431.1 linkuse as main transcriptc.10A>G p.Ile4Val missense_variant 1/39 ENSP00000498149.1 A0A3B3IU05

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000403
AC:
1
AN:
248414
Hom.:
0
AF XY:
0.00000742
AC XY:
1
AN XY:
134814
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000887
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.00000206
AC:
3
AN:
1458030
Hom.:
0
Cov.:
29
AF XY:
0.00000413
AC XY:
3
AN XY:
725562
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000271
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000827
AC:
1
EpiCase
AF:
0.00
EpiControl
AF:
0.0000593

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Pathogenic:1Uncertain:2
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

not provided Uncertain:2
Uncertain significance, criteria provided, single submitterclinical testingGeneDxSep 27, 2019In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
Uncertain significance, criteria provided, single submitterclinical testingAthena DiagnosticsAug 22, 2018- -
Spastic ataxia Pathogenic:1
Likely pathogenic, criteria provided, single submitterresearchMolecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella MarisJul 12, 2021- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.55
BayesDel_addAF
Pathogenic
0.26
D
BayesDel_noAF
Pathogenic
0.14
CADD
Uncertain
25
DANN
Pathogenic
1.0
DEOGEN2
Uncertain
0.57
.;.;.;.;.;.;D;.;.;.
Eigen
Pathogenic
0.86
Eigen_PC
Pathogenic
0.80
FATHMM_MKL
Pathogenic
0.98
D
LIST_S2
Pathogenic
1.0
D;D;D;D;D;D;D;D;.;D
M_CAP
Uncertain
0.10
D
MetaRNN
Pathogenic
0.86
D;D;D;D;D;D;D;D;D;D
MetaSVM
Pathogenic
1.0
D
MutationAssessor
Pathogenic
3.3
M;.;.;.;.;.;M;.;.;.
PrimateAI
Uncertain
0.77
T
PROVEAN
Benign
-0.94
N;N;N;N;.;.;.;.;N;.
REVEL
Pathogenic
0.78
Sift
Pathogenic
0.0
D;D;D;D;.;.;.;.;D;.
Sift4G
Uncertain
0.012
D;D;.;D;.;.;.;.;D;.
Polyphen
0.99
.;.;.;.;.;.;D;.;.;.
Vest4
0.73
MutPred
0.70
Gain of ubiquitination at K890 (P = 0.1103);.;Gain of ubiquitination at K890 (P = 0.1103);.;Gain of ubiquitination at K890 (P = 0.1103);.;Gain of ubiquitination at K890 (P = 0.1103);.;.;.;
MVP
0.90
MPC
1.6
ClinPred
0.88
D
GERP RS
5.1
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7
Varity_R
0.39
gMVP
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.030
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs750473506; hg19: chr3-4716836; API