3-14496541-G-A

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_001080423.4(GRIP2):c.2699C>T(p.Thr900Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 34)
• Consequence: GRIP2 NM_001080423.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.58

Genes affected

GRIP2 (HGNC:23841): (glutamate receptor interacting protein 2) Predicted to enable protein C-terminus binding activity. Predicted to be involved in several processes, including neurotransmitter receptor transport, endosome to postsynaptic membrane; positive regulation of AMPA glutamate receptor clustering; and positive regulation of excitatory postsynaptic potential. Predicted to act upstream of or within Notch signaling pathway; artery smooth muscle contraction; and positive regulation of blood pressure. Predicted to be located in cytoplasm; dendritic shaft; and neuron spine. Predicted to be active in glutamatergic synapse and postsynaptic density. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

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
GRIP2	NM_001080423.4	c.2699C>T	p.Thr900Ile	missense_variant	22/24	ENST00000621039.5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRIP2	ENST00000621039.5	c.2699C>T	p.Thr900Ile	missense_variant	22/24	1	NM_001080423.4	P2
GRIP2	ENST00000619221.4	c.2990C>T	p.Thr997Ile	missense_variant	23/25	5
GRIP2	ENST00000637182.1	c.2714C>T	p.Thr905Ile	missense_variant	22/24	5		A1
GRIP2	ENST00000430219.2	c.*359C>T		3_prime_UTR_variant, NMD_transcript_variant	10/12	2

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 34

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Ambry Genetics

Aug 12, 2021

The c.2990C>T (p.T997I) alteration is located in exon 23 (coding exon 23) of the GRIP2 gene. This alteration results from a C to T substitution at nucleotide position 2990, causing the threonine (T) at amino acid position 997 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.25
BayesDel_addAF	Pathogenic	0.23	D
BayesDel_noAF	Uncertain	0.10
Cadd	Benign	21
Dann	Benign	0.87
DEOGEN2	Benign	0.088	T;.;.
FATHMM_MKL	Benign	0.32	N
LIST_S2	Uncertain	0.89	D;D;D
MetaRNN	Uncertain	0.43	T;T;T
MutationAssessor	Uncertain	2.3	M;.;.
PrimateAI	Uncertain	0.51	T
Sift4G	Uncertain	0.0020	D;D;.
Polyphen		0.40	B;.;.
Vest4		0.47
MVP		0.76
GERP RS		2.9
Varity_R		0.058
gMVP		0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr3-14538049;