NM_000359.3(TGM1):c.1074C>G (p.Ser358Arg) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 1, 2021
Review status:: 1 star out of maximum of 4 stars
criteria provided, single submitter

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:: RCV001070662.6

Allele description [Variation Report for NM_000359.3(TGM1):c.1074C>G (p.Ser358Arg)]

NM_000359.3(TGM1):c.1074C>G (p.Ser358Arg)

Gene:

TGM1:transglutaminase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

14q12

Genomic location:

Preferred name:

NM_000359.3(TGM1):c.1074C>G (p.Ser358Arg)

HGVS:

NC_000014.9:g.24259160G>C
NG_007150.1:g.9007C>G
NM_000359.3:c.1074C>GMANE SELECT
NP_000350.1:p.Ser358Arg
NC_000014.8:g.24728366G>C
NM_000359.2:c.1074C>G

Protein change:

S358R

Links:

dbSNP: rs779287673

NCBI 1000 Genomes Browser:

rs779287673

Molecular consequence:

NM_000359.3:c.1074C>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001235926	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 1, 2021)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 9261103, 27025581, 28403434, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001235926

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 1, 2021)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Citations

PubMed

Consequences of seven novel mutations on the expression and structure of keratinocyte transglutaminase.

Huber M, Yee VC, Burri N, Vikerfors E, Lavrijsen AP, Paller AS, Hohl D.

J Biol Chem. 1997 Aug 22;272(34):21018-26.

PubMed [citation]

PMID:: 9261103

Spectrum of Autosomal Recessive Congenital Ichthyosis in Scandinavia: Clinical Characteristics and Novel and Recurrent Mutations in 132 Patients.

Pigg MH, Bygum A, Gånemo A, Virtanen M, Brandrup F, Zimmer AD, Hotz A, Vahlquist A, Fischer J.

Acta Derm Venereol. 2016 Nov 2;96(7):932-937. doi: 10.2340/00015555-2418.

PubMed [citation]

PMID:: 27025581

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV001235926.5

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt TGM1 protein function. ClinVar contains an entry for this variant (Variation ID: 553856). This missense change has been observed in individual(s) with congenital ichthyosis (PMID: 9261103, 27025581, 28403434). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is present in population databases (rs779287673, gnomAD 0.009%). This sequence change replaces serine, which is neutral and polar, with arginine, which is basic and polar, at codon 358 of the TGM1 protein (p.Ser358Arg).

#	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

Last Updated: Sep 29, 2024

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