NM_001358263.1(HK1):c.19C>T (p.Arg7Ter) AND Charcot-Marie-Tooth disease type 4G

Germline classification:: Pathogenic/Likely pathogenic (3 submissions)
Last evaluated:: Nov 1, 2020
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:: RCV001526839.13

Allele description [Variation Report for NM_001358263.1(HK1):c.19C>T (p.Arg7Ter)]

NM_001358263.1(HK1):c.19C>T (p.Arg7Ter)

Gene:

HK1:hexokinase 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

10q22.1

Genomic location:

Preferred name:

NM_001358263.1(HK1):c.19C>T (p.Arg7Ter)

HGVS:

NC_000010.11:g.69288762C>T
NG_012077.1:g.23763C>T
NM_001322364.2:c.19C>T
NM_001322365.2:c.19C>T
NM_001358263.1:c.19C>T
NM_033497.3:c.19C>T
NM_033498.3:c.19C>T
NM_033500.2:c.-123C>T
NP_001309293.1:p.Arg7Ter
NP_001309294.1:p.Arg7Ter
NP_001345192.1:p.Arg7Ter
NP_277032.1:p.Arg7Ter
NP_277033.1:p.Arg7Ter
LRG_365t1:c.-123C>T
LRG_365:g.23763C>T
NC_000010.10:g.71048518C>T
NM_001322365.1:c.19C>T
NM_001358263.1:c.19C>T
p.R7*

Protein change:

R7*

Links:

dbSNP: rs779250530

NCBI 1000 Genomes Browser:

rs779250530

Molecular consequence:

NM_033500.2:c.-123C>T - 5 prime UTR variant - [Sequence Ontology: SO:0001623]
NM_001322364.2:c.19C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001322365.2:c.19C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001358263.1:c.19C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_033497.3:c.19C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_033498.3:c.19C>T - nonsense - [Sequence Ontology: SO:0001587]

Observations:

Condition(s)

Name:: Charcot-Marie-Tooth disease type 4G
Synonyms:: CHARCOT-MARIE-TOOTH NEUROPATHY, TYPE 4G; Neuropathy, hereditary motor and sensory, Russe type; CHARCOT-MARIE-TOOTH DISEASE, DEMYELINATING, TYPE 4G
Identifiers:: MONDO: MONDO:0011534; MedGen: C1854449; Orphanet: 99953; OMIM: 605285

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001737511	Laboratory of Applied Genomics, Kongju National University	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic (Nov 1, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004047059	Neuberg Centre For Genomic Medicine, NCGM	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely pathogenic	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004809200	Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India	criteria provided, single submitter (ACMG Guidelines, 2015)	Pathogenic	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

SCV001737511

Laboratory of Applied Genomics, Kongju National University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic
(Nov 1, 2020)

germline

clinical testing

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

SCV004047059

Neuberg Centre For Genomic Medicine, NCGM

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely pathogenic

germline

clinical testing

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

SCV004809200

Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India

criteria provided, single submitter

(ACMG Guidelines, 2015)

Pathogenic

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	clinical testing
not provided	unknown	yes	1	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 Laboratory of Applied Genomics, Kongju National University, SCV001737511.1

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

Description

Recessive condition

#	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 Neuberg Centre For Genomic Medicine, NCGM, SCV004047059.1

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

Description

The stop gain variant c.19C>T (p.Arg7Ter) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. This variant is reported with the allele frequency (0.0002%) in the gnomAD and novel in 1000 genome database. This variant is predicted to cause loss of normal protein function through protein truncation. Loss of function variants have been previously reported to be disease causing. For these reasons, this variant has been classified as Likely Pathogenic.

#	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 Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India, SCV004809200.1

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

Last Updated: Oct 26, 2024

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