NM_000125.4(ESR1):c.16C>T (p.His6Tyr) AND not provided

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

Germline classification:: Conflicting interpretations of pathogenicity (3 submissions)
Last evaluated:: Mar 1, 2024
Review status:: criteria provided, conflicting classifications

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:: RCV000884714.13

Allele description

NM_000125.4(ESR1):c.16C>T (p.His6Tyr)

Gene:

ESR1:estrogen receptor 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q25.1

Genomic location:

Preferred name:

NM_000125.4(ESR1):c.16C>T (p.His6Tyr)

HGVS:

NC_000006.12:g.151807928C>T
NG_008493.2:g.156238C>T
NM_000125.4:c.16C>TMANE SELECT
NM_001122740.2:c.16C>T
NM_001122741.2:c.16C>T
NM_001122742.2:c.16C>T
NM_001291230.2:c.16C>T
NM_001291241.2:c.16C>T
NM_001385568.1:c.16C>T
NM_001385569.1:c.16C>T
NM_001385570.1:c.16C>T
NM_001385571.1:c.16C>T
NM_001385572.1:c.16C>T
NP_000116.2:p.His6Tyr
NP_000116.2:p.His6Tyr
NP_001116212.1:p.His6Tyr
NP_001116213.1:p.His6Tyr
NP_001116214.1:p.His6Tyr
NP_001278159.1:p.His6Tyr
NP_001278170.1:p.His6Tyr
NP_001372497.1:p.His6Tyr
NP_001372498.1:p.His6Tyr
NP_001372499.1:p.His6Tyr
NP_001372500.1:p.His6Tyr
NP_001372501.1:p.His6Tyr
LRG_992t1:c.16C>T
LRG_992:g.156238C>T
LRG_992p1:p.His6Tyr
NC_000006.11:g.152129063C>T
NM_000125.3:c.16C>T

Protein change:

H6Y

Links:

dbSNP: rs139960913

NCBI 1000 Genomes Browser:

rs139960913

Molecular consequence:

NM_000125.4:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001122740.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001122741.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001122742.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001291230.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001291241.2:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385568.1:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385569.1:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385570.1:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385571.1:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]
NM_001385572.1:c.16C>T - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001028112	Invitae	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Likely benign (Dec 31, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV001795066	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Oct 30, 2019)	germline	clinical testing	Citation Link,
SCV004160489	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Likely benign (Mar 1, 2024)	germline	clinical testing	Citation Link

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV001028112

Invitae

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Likely benign
(Dec 31, 2019)

germline

clinical testing

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

SCV001795066

GeneDx

criteria provided, single submitter

(GeneDx Variant Classification Process June 2021)

Uncertain significance
(Oct 30, 2019)

germline

clinical testing

Citation Link,

SCV004160489

CeGaT Center for Human Genetics Tuebingen

criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)

Likely benign
(Mar 1, 2024)

germline

clinical testing

Citation Link

Help

Summary from all submissions

Ethnicity	Origin	Affected	Individuals	Families	Chromosomes tested	Number Tested	Family history	Method
not provided	germline	yes	2	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	not provided	not provided	not provided	not provided	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):240-242.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Invitae, SCV001028112.2

#	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 GeneDx, SCV001795066.1

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

Description

Identified in an individual with primary ovarian insufficiency, however, functional studies in HEK293T cells demonstrated that the variant showed similar transcriptional activity to wild type (Bouilly et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 23074960, 27603904)

#	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 CeGaT Center for Human Genetics Tuebingen, SCV004160489.4

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	2	not provided	not provided	clinical testing	not provided

Description

ESR1: PP3, BS2

#	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		2	not provided	not provided	not provided

Last Updated: Apr 15, 2024

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