11-120819840-C-G

Variant names:

• chr11-120819840-C-G
• NM_014619.5:c.431C>G

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_014619.5(GRIK4):​c.431C>G​(p.Thr144Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

• Frequency: Genomes: not found (cov: 32)
• Consequence: GRIK4 NM_014619.5 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 2.60

Genes affected

GRIK4 (HGNC:4582): (glutamate ionotropic receptor kainate type subunit 4) This gene encodes a protein that belongs to the glutamate-gated ionic channel family. Glutamate functions as the major excitatory neurotransmitter in the central nervous system through activation of ligand-gated ion channels and G protein-coupled membrane receptors. The protein encoded by this gene forms functional heteromeric kainate-preferring ionic channels with the subunits encoded by related gene family members. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2013]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.31213465).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
GRIK4	NM_014619.5	c.431C>G	p.Thr144Ser	missense_variant	Exon 6 of 21	ENST00000527524.8	NP_055434.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
GRIK4	ENST00000527524.8	c.431C>G	p.Thr144Ser	missense_variant	Exon 6 of 21	2	NM_014619.5	ENSP00000435648.2
GRIK4	ENST00000438375.2	c.431C>G	p.Thr144Ser	missense_variant	Exon 5 of 20	1		ENSP00000404063.2
GRIK4	ENST00000533291.5	n.829C>G		non_coding_transcript_exon_variant	Exon 6 of 18	1
GRIK4	ENST00000638419.1	c.431C>G	p.Thr144Ser	missense_variant	Exon 6 of 21	5		ENSP00000492086.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

not specified Uncertain:1

Jan 17, 2025

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.431C>G (p.T144S) alteration is located in exon 4 (coding exon 4) of the GRIK4 gene. This alteration results from a C to G substitution at nucleotide position 431, causing the threonine (T) at amino acid position 144 to be replaced by a serine (S). 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	0.083
BayesDel_addAF	Benign	-0.013	T
BayesDel_noAF	Benign	-0.26
CADD	Uncertain	24
DANN	Uncertain	0.99
DEOGEN2	Benign	0.074	T;T;T
Eigen	Benign	0.14
Eigen_PC	Benign	0.21
FATHMM_MKL	Uncertain	0.92	D
LIST_S2	Benign	0.72	.;.;T
M_CAP	Benign	0.064	D
MetaRNN	Benign	0.31	T;T;T
MetaSVM	Benign	-0.32	T
MutationAssessor	Benign	1.5	L;L;L
PrimateAI	Uncertain	0.68	T
PROVEAN	Benign	0.14	N;.;N
REVEL	Uncertain	0.34
Sift	Benign	0.78	T;.;T
Sift4G	Benign	0.70	T;.;T
Polyphen		0.85	P;P;P
Vest4		0.48
MutPred		0.51		Gain of disorder (P = 0.0341);Gain of disorder (P = 0.0341);Gain of disorder (P = 0.0341);
MVP		0.61
MPC		1.1
ClinPred		0.86	D
GERP RS		4.6
Varity_R		0.16
gMVP		0.57

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: chr11-120690549; COSMIC: COSV101483759; COSMIC: COSV101483759;