VCV004467756.1 - ClinVar

NM_002294.3(LAMP2):c.920A>G (p.Asn307Ser)

Germline

No data submitted for germline classification

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Functional data are available for this variant

Variant Details

Identifiers

NM_002294.3(LAMP2):c.920A>G (p.Asn307Ser)

Variation ID: 4467756 Accession: VCV004467756.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: Xq24 X: 120442607 (GRCh38) [ NCBI UCSC ] X: 119576462 (GRCh37) [ NCBI UCSC ]

HGVS

Nucleotide	Protein	Molecular consequence
NM_002294.3:c.920A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_002285.1:p.Asn307Ser	missense
NM_001122606.1:c.920A>G	NP_001116078.1:p.Asn307Ser	missense
NM_013995.2:c.920A>G	NP_054701.1:p.Asn307Ser	missense
NC_000023.11:g.120442607T>C
NC_000023.10:g.119576462T>C
NG_007995.1:g.31743A>G
LRG_749:g.31743A>G
LRG_749t1:c.920A>G	LRG_749p1:p.Asn307Ser
LRG_749t2:c.920A>G	LRG_749p2:p.Asn307Ser
LRG_749t3:c.920A>G	LRG_749p3:p.Asn307Ser

... more HGVS ... less HGVS

Protein change

N307S

Other names

NC_000023.10:g.119576462T>C

Canonical SPDI

NC_000023.11:120442606:T:C

Global minor allele frequency (GMAF) Help The global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

Genes

Gene	OMIM	ClinGen Gene Dosage Sensitivity Curation		Variation Viewer Help Links to Variation Viewer, a genome browser to view variation data from NCBI databases.	Related variants
Gene	OMIM	HI score Help The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.	TS score Help The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team.		Within gene Help The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants.	All Help The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene.
LAMP2		Sufficient evidence for dosage pathogenicity	No evidence available	GRCh38 GRCh37	955	1133

Submissions - Functional Data

functionally abnormal -- retained intron

assessed by RNAseq

Result:

read abundance - intron inclusion (p=0.0457)

Modifies an exonic cryptic donor site at NC_000023.10:g.119576466 from 0.29 to 3.47 bits. Significant p-values: read abundance - intron inclusion (67 reads, p=0.0457). Computations were originally performed using genomic coordinates. This variant was mapped to an appropriate current MANE database designation or, if not present in this source, to the longest relevant transcript in the Biocommons Universal Transcript Archive using the hgvs Python package. The original genomic coordinate was based on GRCh37 and was submitted as an "Alternate designation". Modifications of Figure 2 of PMID:31275557 for ClinVar: a) "strongly corroborating Veridical p-value" refers to "junction-spanning" evidence types; b) add the text "and natural site < 300 nucleotides away?" to "Ri,final > nearest natural site Ri"; c) "Aberrant" and "Likely aberrant" classifications are now both defined as "Functionally abnormal" (analogous to ACMG/AMP reporting); d) "Allele-specific alternative splicing" classification now defined as "Function uncertain" (based on results for similar variants in PMID: 32211018); e) average heterozygosity based-criteria no longer contribute to classification.

Citation: PubMed: 31275557

Dr. Peter K. Rogan Lab, Western University

Accession: SCV006984419.1

Submitted: 2025-10-17

Assay description:

In the sample (TCGA-J8-A3O1), the counts of splice junction spanning reads and abundance of the transcript adjacent to this mutation were compared with RNASeq data from matched tissues and tumors lacking the same mutation using Veridical (PMID:24741438)

Disease context: Thyroid cancer, nonmedullary, 1
Transcript, protein change: NM_002294.3:c.920A>G, N307S
Molecular phenotype measured: splicing
Cell line: TCGA-J8-A3O1
Tissue: Thyroid Carcinoma (THCA)
Collection method: in vitro
Species: human
Number of controls: 536

Text-mined citations for this variant ...

Record last updated Nov 02, 2025