chr9-137161331-AC-TA

Variant names:

• chr9-137161331-AC-TA
• NM_007327.4:c.1382_1383delACinsTA
• GRIN1 p.Asp461Val

GermlineCancer (beta)

Variant summary

Our verdict is Uncertain significance.

+2 Uncertain · Warm

-7

-6

-1

0

+5

+6

+9

+10

BenignB

Likely BenignLB

UncertainVUS

Likely PathogenicLP

PathogenicP

The variant received 2 classification points (ACGS-UK Somatic Oncogenicity v2025). O3_Moderate

The NM_007327.4(GRIN1):c.1382_1383delACinsTA (p.Asp461Val) variant causes a missense change. The gene GRIN1 is a known oncogene (CancerMine: 2 oncogene citations). Note: allele frequency estimates from gnomAD may be inaccurate for this variant type (MNP or indel longer than 3 bp) due to technology limitations. The variant is absent from the gnomAD population database at sites with sufficient sequencing coverage. The affected nucleotide is highly conserved across species (PhyloP 100-way vertebrate score: 8.56). No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Other variants at the same amino acid position have been reported in ClinVar (not pathogenic): p.D461= (synonymous): Likely_benign (ClinVar VariationId 1572773, 1 star); p.D461G: Uncertain_significance (ClinVar VariationId 521271, 2 stars)

• Frequency: Genomes: not found (cov: 32)
• Consequence: GRIN1 NM_007327.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 8.56
• 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 ACGS-UK Somatic Oncogenicity v2025

Classification was made for transcript:

Our verdict: Uncertain_significance. The variant received 2 points.

Apply	Criterion Code & Title / Strength	Strength	Rationale / Clinical Context
	O3Absent or very rare in population		Absent or extremely rare in gnomAD (AC ≤ 2) — O3 moderate; GnomAD: AF = absent, AC = 0 — absent/extremely rare (O3 moderate [+2])

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.1382_1383delACinsTA p.Asp461Val	missense	N/A	Prot: NP_015566.1 UniProt:
	GRIN1 NM_001437330.1		c.1445_1446delACinsTA p.Asp482Val	missense	N/A	Prot: NP_001424259.1 UniProt:
	GRIN1 NM_001185090.2		c.1445_1446delACinsTA p.Asp482Val	missense	N/A	Prot: NP_001172019.1 UniProt:

GRIN1 NM_007327.4

MANE Select

HGVSc / HGVSpc.1382_1383delACinsTAp.Asp461Val

Exon rankN/A

missense

Prot: NP_015566.1UniProt: Q05586-1

GRIN1 NM_001437330.1

HGVSc / HGVSpc.1445_1446delACinsTAp.Asp482Val

Exon rankN/A

missense

Prot: NP_001424259.1UniProt: Q05586-5

GRIN1 NM_001185090.2

HGVSc / HGVSpc.1445_1446delACinsTAp.Asp482Val

Exon rankN/A

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.1382_1383delACinsTA p.Asp461Val	missense	N/A	Prot: ENSP00000360616.3 UniProt:
	GRIN1 ENST00000371553.8	TSL:1	c.1445_1446delACinsTA p.Asp482Val	missense	N/A	Prot: ENSP00000360608.3 UniProt:
	GRIN1 ENST00000371560.5	TSL:1	c.1445_1446delACinsTA p.Asp482Val	missense	N/A	Prot: ENSP00000360615.3 UniProt:

GRIN1 ENST00000371561.8

TSL:1MANE Select

HGVSc / HGVSpc.1382_1383delACinsTAp.Asp461Val

Exon rankN/A

missense

Prot: ENSP00000360616.3UniProt: Q05586-1

GRIN1 ENST00000371553.8

TSL:1

HGVSc / HGVSpc.1445_1446delACinsTAp.Asp482Val

Exon rankN/A

missense

Prot: ENSP00000360608.3UniProt: Q05586-6

GRIN1 ENST00000371560.5

TSL:1

HGVSc / HGVSpc.1445_1446delACinsTAp.Asp482Val

Exon rankN/A

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 2 sources Large-scale international reference populations
GnomAD3 genomes	AF:	AC:	Hom:	AN:	Cov:32
GnomAD4 genome	AF:	AC:	Hom:	AN:	Cov:32

Showing 2 sources

ClinVar

Not reported in ClinVar

Computational Scores

Algorithm	Calibrated pred.	Score	Prediction
PhyloP100	Pathogenic	8.6

Showing 1 of 1 scores

Splicing Scores

No splicing scores have been computed for this variant.

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

hg19: chr9-140055783;

ACMG debug oncogenicity

ACGS debug oncogenicity

ACMG debug germline

Submit to ClinVar