LINGO2 p.Pro217Pro

Variant names:

• chr9-27950020-C-C
• NM_001258282.3:c.

Your query was ambiguous. Multiple possible variants found:

• chr9-27950021--
• chr9-27950021-A-G
• chr9-27950021-A-T
• chr9-27950021-A-C

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_001258282.3(LINGO2):​c. variant causes a exon region change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 32)
• Consequence: LINGO2 NM_001258282.3 exon_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.679
• Publications: 0 publications found

Genes affected

LINGO2 (HGNC:21207): (leucine rich repeat and Ig domain containing 2) Predicted to act upstream of or within positive regulation of synapse assembly. Predicted to be integral component of membrane. Predicted to be active in extracellular matrix and extracellular space. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001258282.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINGO2	NM_001258282.3	MANE Select	c.		exon_region	Exon 7 of 7	NP_001245211.1	Q7L985
	LINGO2	NM_001354574.2		c.		exon_region	Exon 6 of 6	NP_001341503.1	Q7L985
	LINGO2	NM_001354575.2		c.		exon_region	Exon 7 of 7	NP_001341504.1	Q7L985

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINGO2	ENST00000698399.1	MANE Select	c.		exon_region	Exon 7 of 7	ENSP00000513694.1	Q7L985
	LINGO2	ENST00000379992.6	TSL:5	c.		exon_region	Exon 6 of 6	ENSP00000369328.1	Q7L985
	LINGO2	ENST00000698400.1		c.		exon_region	Exon 7 of 7	ENSP00000513695.1	Q7L985

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 32

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.68

Splicing

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.

Other links and lift over

hg19: chr9-27950018;