NM_000359.3(TGM1):c.1645+1G>T AND Autosomal recessive congenital ichthyosis 1

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Mar 18, 2024
Review status:: 2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts

Somatic classification of clinical impact:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Somatic classification of oncogenicity:: None
Review status:: (0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided

Record status:: current
Accession:: RCV002267141.6

Allele description [Variation Report for NM_000359.3(TGM1):c.1645+1G>T]

NM_000359.3(TGM1):c.1645+1G>T

Gene:

TGM1:transglutaminase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q12

Genomic location:

Preferred name:

NM_000359.3(TGM1):c.1645+1G>T

HGVS:

NC_000014.9:g.24255363C>A
NG_007150.2:g.12804G>T
NM_000359.3:c.1645+1G>TMANE SELECT
NC_000014.8:g.24724569C>A

Links:

dbSNP: rs774242987

NCBI 1000 Genomes Browser:

rs774242987

Molecular consequence:

NM_000359.3:c.1645+1G>T - splice donor variant - [Sequence Ontology: SO:0001575]

Observations:

Condition(s)

Name:: Autosomal recessive congenital ichthyosis 1 (LI1)
Synonyms:: COLLODION FETUS; DESQUAMATION OF NEWBORN; ICHTHYOSIS CONGENITA; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0009441; MedGen: C4551630; OMIM: 242300

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002549127	Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jun 23, 2022)	paternal	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV002763021	Genome-Nilou Lab	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004203824	Baylor Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Mar 18, 2024)	unknown	clinical testing	PubMed (1) [See all records that cite this PMID]

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV002549127

Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jun 23, 2022)

paternal

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV002763021

Genome-Nilou Lab

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004203824

Baylor Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Mar 18, 2024)

unknown

clinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	paternal	yes	1	not provided	not provided	not provided	not provided	clinical testing
not provided	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee.

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen, SCV002549127.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1		1	not provided	not provided	clinical testing	PubMed (1)

Description

The detected change is reported in the dbSNP database (dbSNP151 as of 06/23/2022) with the designation rs774242987. In gnomAD it is listed with a frequency of 0.001061% (3/282686) (as of 06/23/2022). The change affects the canonical splice site and in all likelihood leads to altered splicing and usually to loss of function of the corresponding protein. The variant is currently to be regarded as a "pathogenic variant" (ACMG criteria).

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	paternal	yes	not provided	not provided	not provided		1	not provided	not provided	not provided

From Genome-Nilou Lab, SCV002763021.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	germline	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

From Baylor Genetics, SCV004203824.2

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (1)

#	Sample				Method		Observation
#	Origin	Affected	Number tested	Tissue	Purpose	Method	Individuals	Allele frequency	Families	Co-occurrences
1	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Apr 13, 2025

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