NM_005554.4(KRT6A):c.1414G>A (p.Glu472Lys) AND Pachyonychia congenita 3

Germline classification:: Likely pathogenic (2 submissions)
Last evaluated:: Jan 17, 2022
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:: RCV000015742.29

Allele description [Variation Report for NM_005554.4(KRT6A):c.1414G>A (p.Glu472Lys)]

NM_005554.4(KRT6A):c.1414G>A (p.Glu472Lys)

Gene:

KRT6A:keratin 6A [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

12q13.13

Genomic location:

Preferred name:

NM_005554.4(KRT6A):c.1414G>A (p.Glu472Lys)

HGVS:

NC_000012.12:g.52488338C>T
NG_008298.1:g.10060G>A
NM_005554.4:c.1414G>AMANE SELECT
NP_005545.1:p.Glu472Lys
LRG_1294t1:c.1414G>A
LRG_1294:g.10060G>A
LRG_1294p1:p.Glu472Lys
NC_000012.11:g.52882122C>T
NM_005554.3:c.1414G>A
P02538:p.Glu472Lys

Protein change:

E472K; GLU472LYS

Links:

UniProtKB: P02538#VAR_017077; OMIM: 148041.0003; dbSNP: rs60554162

NCBI 1000 Genomes Browser:

rs60554162

Molecular consequence:

NM_005554.4:c.1414G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Pachyonychia congenita 3 (PC3)
Synonyms:: PC-K6a
Identifiers:: MONDO: MONDO:0014324; MedGen: C3714948; Orphanet: 2309; OMIM: 615726

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SAMEA104177944 (1)
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Sordariomycetes beta-tubulin gene, partial sequence.
Sordariomycetes beta-tubulin gene, partial sequence.
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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000036007	OMIM	no assertion criteria provided	Pathogenic (Dec 1, 2001)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002777429	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic (Jan 17, 2022)	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

SCV000036007

OMIM

no assertion criteria provided

Pathogenic
(Dec 1, 2001)

germline

literature only

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

SCV002777429

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic
(Jan 17, 2022)

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	unknown	unknown	not provided	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	not provided	not provided	not provided	not provided	not provided	not provided	literature only

Citations

PubMed

Novel and recurrent mutations in the genes encoding keratins K6a, K16 and K17 in 13 cases of pachyonychia congenita.

Terrinoni A, Smith FJ, Didona B, Canzona F, Paradisi M, Huber M, Hohl D, David A, Verloes A, Leigh IM, Munro CS, Melino G, McLean WH.

J Invest Dermatol. 2001 Dec;117(6):1391-6.

PubMed [citation]

PMID:: 11886499

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 OMIM, SCV000036007.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	literature only	PubMed (1)

Description

In a patient with sporadic PC (PC3; 615726), Terrinoni et al. (2001) identified a c.1414G-to-A transition in the KRT6A gene that resulted in a glu472-to-lys (E472K) amino acid substitution. This mutation is E117K in the 2B domain of the protein.

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

From Fulgent Genetics, Fulgent Genetics, SCV002777429.1

#	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	unknown	unknown	not provided	not provided	not provided		not provided	not provided	not provided	not provided

Last Updated: Jan 7, 2023

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