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NM_000424.4(KRT5):c.1400T>C (p.Ile467Thr) AND not provided

Germline classification:
Pathogenic (3 submissions)
Last evaluated:
Jul 18, 2023
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:
RCV000056556.3

Allele description [Variation Report for NM_000424.4(KRT5):c.1400T>C (p.Ile467Thr)]

NM_000424.4(KRT5):c.1400T>C (p.Ile467Thr)

Genes:
LOC126861525:BRD4-independent group 4 enhancer GRCh37_chr12:52909857-52911056 [Gene]
KRT5:keratin 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
12q13.13
Genomic location:
Preferred name:
NM_000424.4(KRT5):c.1400T>C (p.Ile467Thr)
HGVS:
  • NC_000012.12:g.52516676A>G
  • NG_008297.1:g.8784T>C
  • NM_000424.4:c.1400T>CMANE SELECT
  • NP_000415.2:p.Ile467Thr
  • NC_000012.11:g.52910460A>G
  • NM_000424.3:c.1400T>C
  • P13647:p.Ile467Thr
Protein change:
I467T
Links:
UniProtKB: P13647#VAR_010466; dbSNP: rs60271599
NCBI 1000 Genomes Browser:
rs60271599
Molecular consequence:
  • NM_000424.4:c.1400T>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
OriginMethodCitations
SCV000087667Epithelial Biology; Institute of Medical Biology, Singapore
no classification provided
not providednot providednot provided

SCV000568716GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))
Pathogenic
(Jan 10, 2017)
germlineclinical testing

Citation Link,

SCV004294170Labcorp Genetics (formerly Invitae), Labcorp
criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))
Pathogenic
(Jul 18, 2023)
germlineclinical testing

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

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing
not providedgermlineunknownnot providednot providednot providednot providednot providedclinical testing
not providednot providednot providednot providednot providednot provided1not providedliterature only

Citations

PubMed

Epidermolysis bullosa simplex in Scotland caused by a spectrum of keratin mutations.

Rugg EL, Horn HM, Smith FJ, Wilson NJ, Hill AJ, Magee GJ, Shemanko CS, Baty DU, Tidman MJ, Lane EB.

J Invest Dermatol. 2007 Mar;127(3):574-80. Epub 2006 Oct 12.

PubMed [citation]
PMID:
17039244
See all PubMed Citations (4)

Details of each submission

From Epithelial Biology; Institute of Medical Biology, Singapore, SCV000087667.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providednot providednot provided
#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1not providednot provided1not providednot providednot providednot providednot providednot provided

From GeneDx, SCV000568716.4

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

The I467T pathogenic variant has been reported previously in association with epidermolysis bullosa simplex (Irvine et al. 1997, Arin et al. 2010). It was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. This substitution occurs within a known mutational hotspot region helix termination motif of the coil 2B region of the protein that is highly conserved across all species and among all members of the keratin family. Many other pathogenic variants in patients with epidermolysis bullosa simplex have been reported in the same residue (I467K, I467L, I467M) and in nearby residues (L463P, E466D, T469P, Y470H, R471C, R471H) according to the Human Gene Mutation Database (Stenson et al., 2014). It is well established that keratin gene mutations affecting the residues at the ends of the central rod domains of the keratin proteins (helix initiation and termination motifs) interfere with proper keratin intermediate filament assembly and function, resulting in skin fragility, blistering and/or hyperkeratosis (Chamcheu et al., 2011). Therefore, I467T is pathogenic and consistent with a diagnosis of epidermolysis bullosa simplex (EBS).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot providednot providednot providednot providednot provided

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004294170.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (4)

Description

For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Ile467 amino acid residue in KRT5. Other variant(s) that disrupt this residue have been observed in individuals with KRT5-related conditions (PMID: 16098032, 17039244), which suggests that this may be a clinically significant amino acid residue. 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 KRT5 protein function. ClinVar contains an entry for this variant (Variation ID: 66210). This variant is also known as I466T. This missense change has been observed in individual(s) with autosomal dominant epidermolysis bullosa simplex (PMID: 9406827). In at least one individual the variant was observed to be de novo. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces isoleucine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 467 of the KRT5 protein (p.Ile467Thr).

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Sep 29, 2024