chr2-77518865-C-T

Variant names:

• chr2-77518865-C-T
• NM_001134745.3:c.1004G>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001134745.3(LRRTM4):​c.1004G>A​(p.Ser335Asn) variant causes a missense change. The variant allele was found at a frequency of 0.00000138 in 1,454,272 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S335I) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: LRRTM4 NM_001134745.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.67

Genes affected

LRRTM4 (HGNC:19411): (leucine rich repeat transmembrane neuronal 4) Predicted to enable heparan sulfate proteoglycan binding activity. Predicted to be involved in regulation of synapse assembly. Predicted to act upstream of or within AMPA glutamate receptor clustering; positive regulation of synapse assembly; and regulation of presynaptic membrane organization. Predicted to be located in postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in extracellular matrix; extracellular space; and glutamatergic synapse. Predicted to be integral component of postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.18445706).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LRRTM4	NM_001134745.3	c.1004G>A	p.Ser335Asn	missense_variant	Exon 3 of 4	ENST00000409884.6	NP_001128217.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LRRTM4	ENST00000409884.6	c.1004G>A	p.Ser335Asn	missense_variant	Exon 3 of 4	1	NM_001134745.3	ENSP00000387297.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000138 AC: 2 AN: 1454272 Hom.: 0 Cov.: 35 AF XY: 0.00000277 AC XY: 2 AN XY: 722722

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.11
BayesDel_addAF	Benign	-0.16	T
BayesDel_noAF	Benign	-0.47
CADD	Benign	18
DANN	Benign	0.94
DEOGEN2	Benign	0.0040	T;T;T;.;T
Eigen	Benign	-0.045
Eigen_PC	Benign	0.16
FATHMM_MKL	Uncertain	0.87	D
LIST_S2	Uncertain	0.88	D;.;D;D;D
M_CAP	Benign	0.0054	T
MetaRNN	Benign	0.18	T;T;T;T;T
MetaSVM	Benign	-0.99	T
MutationAssessor	Benign	1.3	.;L;L;L;.
PrimateAI	Uncertain	0.77	T
PROVEAN	Benign	-0.21	N;N;N;N;N
REVEL	Benign	0.088
Sift	Benign	0.52	T;T;T;T;T
Sift4G	Benign	0.56	T;T;T;T;T
Polyphen		0.011, 0.0020, 0.0030	.;B;B;B;B
Vest4		0.43
MutPred		0.29		.;Loss of glycosylation at S335 (P = 0.0982);Loss of glycosylation at S335 (P = 0.0982);Loss of glycosylation at S335 (P = 0.0982);.;
MVP		0.12
MPC		0.85
ClinPred		0.62	D
GERP RS		5.7
Varity_R		0.19
gMVP		0.43

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: chr2-77745991;