NM_005554.4(KRT6A):c.513C>A (p.Asn171Lys) AND Pachyonychia congenita 3

Germline classification:: Pathogenic (3 submissions)
Last evaluated:: Jul 16, 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:: RCV000128821.14

Allele description [Variation Report for NM_005554.4(KRT6A):c.513C>A (p.Asn171Lys)]

NM_005554.4(KRT6A):c.513C>A (p.Asn171Lys)

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.513C>A (p.Asn171Lys)

HGVS:

NC_000012.12:g.52492676G>T
NG_008298.1:g.5722C>A
NM_005554.4:c.513C>AMANE SELECT
NP_005545.1:p.Asn171Lys
LRG_1294t1:c.513C>A
LRG_1294:g.5722C>A
LRG_1294p1:p.Asn171Lys
NC_000012.11:g.52886460G>T
NM_005554.3:c.513C>A
P02538:p.Asn171Lys

Protein change:

N171K; ASN171LYS

Links:

UniProtKB: P02538#VAR_072451; OMIM: 148041.0007; dbSNP: rs59685571

NCBI 1000 Genomes Browser:

rs59685571

Molecular consequence:

NM_005554.4:c.513C>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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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000172479	GeneReviews	no classification provided	not provided	germline	literature only
SCV000189152	OMIM	no assertion criteria provided	Pathogenic (Oct 1, 2005)	germline	literature only	PubMed (1) [See all records that cite this PMID]
SCV002786521	Fulgent Genetics, Fulgent Genetics	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Jul 16, 2021)	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

SCV000172479

GeneReviews

no classification provided

not provided

germline

literature only

SCV000189152

OMIM

no assertion criteria provided

Pathogenic
(Oct 1, 2005)

germline

literature only

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

SCV002786521

Fulgent Genetics, Fulgent Genetics

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Jul 16, 2021)

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

Citations

PubMed

The genetic basis of pachyonychia congenita.

Smith FJ, Liao H, Cassidy AJ, Stewart A, Hamill KJ, Wood P, Joval I, van Steensel MA, Björck E, Callif-Daley F, Pals G, Collins P, Leachman SA, Munro CS, McLean WH.

J Investig Dermatol Symp Proc. 2005 Oct;10(1):21-30. Review.

PubMed [citation]

PMID:: 16250206

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 GeneReviews, SCV000172479.3

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

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

From OMIM, SCV000189152.1

#	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 from a family with pachyonychia congenita (PC3; 615726), Smith et al. (2005) identified heterozygosity for a c.513C-A transversion in the KRT6A gene, resulting in an asn171-to-lys (N171K) substitution in the highly conserved helix initiation motif of the 1A domain.

#	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, SCV002786521.1

#	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: Oct 8, 2024

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