chr9-137163645-C-T

Variant names:

• chr9-137163645-C-T
• rs1554770590
• NM_007327.4:c.2420C>T
• GRIN1 p.Thr807Ile

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+5 Uncertain · Hot

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 5 classification points (ACMG Germline Pathogenicity v2019). PM1PM2PP5

The NM_007327.4(GRIN1):c.2420C>T (p.Thr807Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. Splicing prediction tools (SpliceAI) predict no significant impact on normal splicing. Variant has been reported in ClinVar as Pathogenic/Likely Pathogenic (no review stars). Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.T807S: Uncertain_significance (ClinVar VariationId 4539911, 1 star)

• Frequency: Genomes: not found (cov: 33)
• Consequence: GRIN1 NM_007327.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications P:1 U:1
• Conservation: PhyloP100: 5.47
• Publications: 0 publications found

Genes affected

GRIN1 (HGNC:4584): (glutamate ionotropic receptor NMDA type subunit 1) The protein encoded by this gene is a critical subunit of N-methyl-D-aspartate receptors, members of the glutamate receptor channel superfamily which are heteromeric protein complexes with multiple subunits arranged to form a ligand-gated ion channel. These subunits play a key role in the plasticity of synapses, which is believed to underlie memory and learning. Cell-specific factors are thought to control expression of different isoforms, possibly contributing to the functional diversity of the subunits. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2008]

GRIN1 Gene-Disease associations (from GenCC):

• neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant

  Inheritance: AD Classification: DEFINITIVE, STRONG, MODERATE Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
• complex neurodevelopmental disorder

  Inheritance: AR, AD Classification: DEFINITIVE Submitted by: ClinGen
• neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal recessive

  Inheritance: AR Classification: DEFINITIVE, MODERATE Submitted by: G2P, Ambry Genetics
• developmental and epileptic encephalopathy 101

  Inheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
• GRIN1-related complex neurodevelopmental disorder

  Inheritance: AR Classification: STRONG Submitted by: PanelApp Australia
• autosomal dominant non-syndromic intellectual disability

  Inheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 5 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	PM1Mutational hot spot or critical domain		Missense neighbourhood hotspot (≥2 P/LP within ±8 AA, OR ≥ 5 vs. background) — PM1; In-domain: 0 pathogenic, 0 benign rare missense variants.; ±8 AA neighbourhood: 9 pathogenic, 0 benign (OR vs. background: 95.0).
	PM2Absent/extremely low in population databases		Absent from gnomAD (AD/XL gene) — PM2; Absent from gnomAD at well-covered site (MOI: AD+AR) (threshold 0.0001) — PM2 moderate.
	PP5Reputable source reports pathogenic		ClinVar 0-star pathogenic — supporting (PP5); ClinVar germline classification: Pathogenic/Likely Pathogenic, 0 star(s).

Variant Effect in Transcripts

Automated classification analysis was done for transcript: NM_007327.4. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	GRIN1 NM_007327.4	MANE Select	c.2420C>T p.Thr807Ile	missense	Exon 17 of 20	Prot: NP_015566.1 UniProt:
	GRIN1 NM_001437330.1		c.2483C>T p.Thr828Ile	missense	Exon 18 of 21	Prot: NP_001424259.1 UniProt:
	GRIN1 NM_001185090.2		c.2483C>T p.Thr828Ile	missense	Exon 18 of 21	Prot: NP_001172019.1 UniProt:

GRIN1 NM_007327.4

MANE Select

HGVSc / HGVSpc.2420C>Tp.Thr807Ile

Exon rankExon 17 of 20

missense

Prot: NP_015566.1UniProt: Q05586-1

GRIN1 NM_001437330.1

HGVSc / HGVSpc.2483C>Tp.Thr828Ile

Exon rankExon 18 of 21

missense

Prot: NP_001424259.1UniProt: Q05586-5

GRIN1 NM_001185090.2

HGVSc / HGVSpc.2483C>Tp.Thr828Ile

Exon rankExon 18 of 21

missense

Prot: NP_001172019.1UniProt: Q05586-6

Ensembl Transcripts

Sel.	Gene / Transcript	Tags	HGVSc / HGVSp	Effect	Exon rank	Protein / UniProt
	GRIN1 ENST00000371561.8	TSL:1MANE Select	c.2420C>T p.Thr807Ile	missense	Exon 17 of 20	Prot: ENSP00000360616.3 UniProt:
	GRIN1 ENST00000371553.8	TSL:1	c.2483C>T p.Thr828Ile	missense	Exon 18 of 21	Prot: ENSP00000360608.3 UniProt:
	GRIN1 ENST00000371560.5	TSL:1	c.2483C>T p.Thr828Ile	missense	Exon 18 of 20	Prot: ENSP00000360615.3 UniProt:

GRIN1 ENST00000371561.8

TSL:1MANE Select

HGVSc / HGVSpc.2420C>Tp.Thr807Ile

Exon rankExon 17 of 20

missense

Prot: ENSP00000360616.3UniProt: Q05586-1

GRIN1 ENST00000371553.8

TSL:1

HGVSc / HGVSpc.2483C>Tp.Thr828Ile

Exon rankExon 18 of 21

missense

Prot: ENSP00000360608.3UniProt: Q05586-6

GRIN1 ENST00000371560.5

TSL:1

HGVSc / HGVSpc.2483C>Tp.Thr828Ile

Exon rankExon 18 of 20

missense

Prot: ENSP00000360615.3UniProt: Q05586-7

Frequencies

Allele frequencies (AF), counts (AC/AN), homozygotes and coverage

Common (AF > 0.05 / Hom > 5)

Rare (AF ≤ 0.0001 / Hom ≤ 1)

Source / population	AF	AC	Hom	AN	Coverage
Global population databases 3 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:33
GnomAD4 exome	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:33

Showing 3 sources

ClinVar

ClinVar submissions

Significance: Conflicting classifications of pathogenicity

Revision: criteria provided, conflicting classifications

Pathogenic	VUS	Benign	Condition
-	1	-	Inborn genetic diseases (1)
1	-	-	Neurodevelopmental disorder with or without hyperkinetic movements and seizures, autosomal dominant (1)

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
AlphaGenome AVI	Pathogenic	30
AlphaMissense	Pathogenic	0.99
BayesDel_addAF	Uncertain	0.057	T
BayesDel_noAF	Benign	-0.16
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.84	D
Eigen	Uncertain	0.58
Eigen_PC	Uncertain	0.49
FATHMM_MKL	Uncertain	0.81	D
FuncVEP CTI	Pathogenic	0.95
GPN-Star LLR	N/A	-8.2
GPN-Star score	N/A	8.2
LIST_S2	Uncertain	0.94	D
M_CAP	Pathogenic	0.36	D
MetaRNN	Uncertain	0.56	D
MetaSVM	Uncertain	-0.19	T
Mutation Taster	N/A	20/80	disease causing
MutationAssessor	Uncertain	2.7	M
PhyloP100	Uncertain	5.5
popEVE	Uncertain	-4.9
PrimateAI	Uncertain	0.76	T
PROVEAN	Pathogenic	-5.1	D
REVEL	Uncertain	0.38
Sift	Uncertain	0.0070	D
Sift4G	Uncertain	0.0050	D
Varity_R	N/A	0.85
VESM-3B	Benign	-10

Showing 28 of 28 scores

Splicing Scores

Algorithm	Calibrated pred.	Score	Prediction
Pangolin (max)	Benign	0.0
SpliceAI score (max)	Benign	0.0	Details are displayed if max score is > 0.2

Showing 2 of 2 scores

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

MaveDB functional evidence

MaveDB is a public repository of laboratory assays that test the effect of thousands of variants at once — treat this as supporting research data and interpret it with great caution; it is not a clinical classification.

No MaveDB functional evidence found for this variant.

Other links and lift over

dbSNP: rs1554770590;

hg19: chr9-140058097;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar