ENST00000448413.5:n.1015-129524T>A

Variant names:

• chr3-4505869-T-.
• NM_001378452.1:c.-16-10607T>.

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001378452.1(ITPR1):​c.-16-10607T>. variant causes a intron change. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 N/A (N/A hom., cov:)
  • Exomes 𝑓: N/A (N/A hom.)
• Consequence: ITPR1 NM_001378452.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: No publications found

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]

ITPR1 Gene-Disease associations (from GenCC):

• aniridia-cerebellar ataxia-intellectual disability syndrome

  Inheritance: AD, AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Ambry Genetics, G2P, Genomics England PanelApp, PanelApp Australia, Labcorp Genetics (formerly Invitae), Orphanet, ClinGen
• spinocerebellar ataxia type 29

  Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), G2P, ClinGen, Orphanet
• spinocerebellar ataxia type 15/16

  Inheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Labcorp Genetics (formerly Invitae)

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITPR1	NM_001378452.1	c.-16-10607T>.		intron_variant	Intron 2 of 61	ENST00000649015.2	NP_001365381.1
ITPR1	NM_001168272.2	c.-16-10607T>.		intron_variant	Intron 2 of 60		NP_001161744.1
ITPR1	NM_001099952.4	c.-16-10607T>.		intron_variant	Intron 2 of 58		NP_001093422.2
ITPR1	NM_002222.7	c.-16-10607T>.		intron_variant	Intron 2 of 57		NP_002213.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITPR1	ENST00000649015.2	c.-16-10607T>.		intron_variant	Intron 2 of 61		NM_001378452.1	ENSP00000497605.1
ITPR1	ENST00000354582.12	c.-16-10607T>.		intron_variant	Intron 2 of 61	5		ENSP00000346595.8
ITPR1	ENST00000648266.1	c.-16-10607T>.		intron_variant	Intron 2 of 61			ENSP00000498014.1
ITPR1	ENST00000650294.1	c.-16-10607T>.		intron_variant	Intron 2 of 60			ENSP00000498056.1
ITPR1	ENST00000443694.5	c.-16-10607T>.		intron_variant	Intron 2 of 60	1		ENSP00000401671.2
ITPR1	ENST00000357086.10	c.-16-10607T>.		intron_variant	Intron 2 of 58	1		ENSP00000349597.4
ITPR1	ENST00000456211.8	c.-16-10607T>.		intron_variant	Intron 2 of 57	1		ENSP00000397885.2

Frequencies

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

We have no GnomAD4 genomes data on this position. Probably position not covered by the project.

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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

Other links and lift over

hg19: chr3-4547553;