VCV001699950.2 - ClinVar

LAMA3, IVS35, +1, G-A

Germline

Classification

The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.

(2)

Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.

Pathogenic

no assertion criteria provided

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

LAMA3, IVS35, +1, G-A

Variation ID: 1699950 Accession: VCV001699950.2

Type and length

single nucleotide variant, -

Location

Timeline in ClinVar

	First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.	Last submission Help The date of the most recent submission for each type of classification for this variant.	Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline	Aug 8, 2022	Dec 9, 2023	Jan 1, 2002

HGVS

Protein change

Other names

IVS35, +1, G-A

Canonical SPDI

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

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

OMIM: 600805.0006

Comment on variant

NCBI staff could not provide an HGVS expression for allelic variant 600805.0006 because the numbering system used to define the location was not clear.

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.
LAMA3		-	-	GRCh38 GRCh37	1879	1970

Conditions - Germline

Condition Help The condition for this variant-condition (RCV) record in ClinVar.	Classification Help The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions)	Review status Help The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status.	Last evaluated Help The most recent date that a submitter evaluated this variant for the condition.	Variation/condition record Help The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page.
Epidermolysis bullosa, junctional 2A, intermediate	Pathogenic (1)	no assertion criteria provided	Jan 1, 2002	RCV002273910.2
Laryngo-onycho-cutaneous syndrome	Pathogenic (1)	no assertion criteria provided	Jan 1, 2002	RCV003445158.1

Submissions - Germline

Classification Help The submitted germline classification for each SCV record. (Last evaluated)	Review status Help Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria)	Condition Help The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant.	Submitter Help The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar.	More information Help This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter.
Pathogenic (Jan 01, 2002)	no assertion criteria provided Method: literature only	EPIDERMOLYSIS BULLOSA, JUNCTIONAL 2C, LARYNGOONYCHOCUTANEOUS Affected status: not provided Allele origin: germline	OMIM Accession: SCV004174173.1 First in ClinVar: Dec 09, 2023 Last updated: Dec 09, 2023	Publications: PubMed (2) PubMed: 11810295‚ 17362460 Comment on evidence: Intermediate Junctional Epidermolysis Bullosa 2A For discussion of the splice donor mutation (c.4651+1G-A) in intron 35 of the LAMA3 gene that was found in compound … (more) Intermediate Junctional Epidermolysis Bullosa 2A For discussion of the splice donor mutation (c.4651+1G-A) in intron 35 of the LAMA3 gene that was found in compound heterozygous state in a patient with intermediate junctional epidermolysis bullosa 2A (JEB2A; 619783) by Nakano et al. (2002), see 600805.0005. Laryngoonychocutaneous Junctional Epidermolysis Bullosa 2C In a 7-year-old boy with laryngoonychocutaneous junctional epidermolysis bullosa 2C (JEB2C; 245660) Figueira et al. (2007) identified compound heterozygosity for mutations in the LAMA3 gene: a paternally inherited splice site mutation at the donor site of intron 35 (c.4651+1G-A), and a maternally inherited missense mutation, ile17-to-asn (600805.0009), that affected the laminin alpha-3a (LAMA3A) isoform. (less)
Pathogenic (Jan 01, 2002)	no assertion criteria provided Method: literature only	EPIDERMOLYSIS BULLOSA, JUNCTIONAL 2A, INTERMEDIATE Affected status: not provided Allele origin: germline	OMIM Accession: SCV002558751.2 First in ClinVar: Aug 08, 2022 Last updated: Dec 09, 2023	Publications: PubMed (2) PubMed: 11810295‚ 17362460 Comment on evidence: Intermediate Junctional Epidermolysis Bullosa 2A For discussion of the splice donor mutation (c.4651+1G-A) in intron 35 of the LAMA3 gene that was found in compound … (more) Intermediate Junctional Epidermolysis Bullosa 2A For discussion of the splice donor mutation (c.4651+1G-A) in intron 35 of the LAMA3 gene that was found in compound heterozygous state in a patient with intermediate junctional epidermolysis bullosa 2A (JEB2A; 619783) by Nakano et al. (2002), see 600805.0005. Laryngoonychocutaneous Junctional Epidermolysis Bullosa 2C In a 7-year-old boy with laryngoonychocutaneous junctional epidermolysis bullosa 2C (JEB2C; 245660) Figueira et al. (2007) identified compound heterozygosity for mutations in the LAMA3 gene: a paternally inherited splice site mutation at the donor site of intron 35 (c.4651+1G-A), and a maternally inherited missense mutation, ile17-to-asn (600805.0009), that affected the laminin alpha-3a (LAMA3A) isoform. (less)

Germline Functional Evidence

There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar.

Citations for germline classification of this variant

Title	Author	Journal	Year	Link
Granulation tissue in the eyelid margin and conjunctiva in junctional epidermolysis bullosa with features of laryngo-onycho-cutaneous syndrome.	Figueira EC	Clinical & experimental ophthalmology	2007	PMID: 17362460
Laminin 5 mutations in junctional epidermolysis bullosa: molecular basis of Herlitz vs. non-Herlitz phenotypes.	Nakano A	Human genetics	2002	PMID: 11810295

Text-mined citations for this variant ...

Record last updated Dec 09, 2023

ClinVar Genomic variation as it relates to human health

LAMA3, IVS35, +1, G-A

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...