NM_000238.4(KCNH2):c.2994C>T (p.Phe998=) AND Long QT syndrome

This record was updated by the submitter. Please see the current version.

Germline classification:: Likely benign (2 submissions)
Last evaluated:: Jan 15, 2024
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:: RCV000545645.19

Allele description

NM_000238.4(KCNH2):c.2994C>T (p.Phe998=)

Gene:

KCNH2:potassium voltage-gated channel subfamily H member 2 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

7q36.1

Genomic location:

Preferred name:

NM_000238.4(KCNH2):c.2994C>T (p.Phe998=)

Other names:

p.F998F:TTC>TTT

HGVS:

NC_000007.14:g.150947486G>A
NG_008916.1:g.35441C>T
NM_000238.4:c.2994C>TMANE SELECT
NM_172057.3:c.1974C>T
NP_000229.1:p.Phe998=
NP_000229.1:p.Phe998=
NP_742054.1:p.Phe658=
LRG_288t1:c.2994C>T
LRG_288:g.35441C>T
LRG_288p1:p.Phe998=
NC_000007.13:g.150644574G>A
NM_000238.2:c.2994C>T
NM_000238.3:c.2994C>T

Links:

dbSNP: rs368954514

NCBI 1000 Genomes Browser:

rs368954514

Molecular consequence:

NM_000238.4:c.2994C>T - synonymous variant - [Sequence Ontology: SO:0001819]
NM_172057.3:c.1974C>T - synonymous variant - [Sequence Ontology: SO:0001819]

Observations:

Condition(s)

Name:: Long QT syndrome (LQTS)
Identifiers:: MONDO: MONDO:0002442; MeSH: D008133; MedGen: C0023976

Recent activity

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nad52c08.x1 NCI_CGAP_Lu24 Homo sapiens cDNA clone IMAGE:3407222 3', mRNA sequenc...
nad52c08.x1 NCI_CGAP_Lu24 Homo sapiens cDNA clone IMAGE:3407222 3', mRNA sequence
gi|12513631|gnl|dbEST|7619206|gb|BG 7.1|

Nucleotide
PREDICTED: Mus musculus nuclear factor of activated T cells 5 (Nfat5), transcrip...
PREDICTED: Mus musculus nuclear factor of activated T cells 5 (Nfat5), transcript variant X16, mRNA
gi|1907190404|ref|XM_036154184.1|

Nucleotide
Klebsiella variicola strain 3KXXI NODE_84_length_5444_cov_50.448668, whole genom...
Klebsiella variicola strain 3KXXI NODE_84_length_5444_cov_50.448668, whole genome shotgun sequence
gi|2035655668|ref|NZ_JAAGZV01000008 gnl|WGS:NZ_JAAGZV01|NODE_84_length_5444_cov_50.448668

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000627472	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Jan 15, 2024)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004835889	All of Us Research Program, National Institutes of Health	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely Benign (Nov 30, 2023)	germline	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

SCV000627472

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Jan 15, 2024)

germline

clinical testing

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

SCV004835889

All of Us Research Program, National Institutes of Health

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely Benign
(Nov 30, 2023)

germline

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	unknown	17	not provided	not provided	108544	not provided	clinical testing

Citations

PubMed

Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria.

Nykamp K, Anderson M, Powers M, Garcia J, Herrera B, Ho YY, Kobayashi Y, Patil N, Thusberg J, Westbrook M; Invitae Clinical Genomics Group., Topper S.

Genet Med. 2017 Oct;19(10):1105-1117. doi: 10.1038/gim.2017.37. Epub 2017 May 11. Erratum in: Genet Med. 2020 Jan;22(1):240. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

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 Invitae, SCV000627472.7

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

From All of Us Research Program, National Institutes of Health, SCV004835889.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	17	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	germline	unknown	108544	not provided	not provided		17	not provided	not provided	not provided

Last Updated: Sep 16, 2024

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