NM_182961.4(SYNE1):c.26330C>G (p.Ser8777Cys) AND not provided

Germline classification:: Uncertain significance (5 submissions)
Last evaluated:: Feb 1, 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:: RCV000727476.26

Allele description [Variation Report for NM_182961.4(SYNE1):c.26330C>G (p.Ser8777Cys)]

NM_182961.4(SYNE1):c.26330C>G (p.Ser8777Cys)

Genes:

ESR1:estrogen receptor 1 [Gene - OMIM - HGNC]
SYNE1:spectrin repeat containing nuclear envelope protein 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

6q25.2

Genomic location:

Preferred name:

NM_182961.4(SYNE1):c.26330C>G (p.Ser8777Cys)

HGVS:

NC_000006.12:g.152122500G>C
NG_008493.2:g.470810G>C
NG_012855.2:g.519900C>G
NM_001328100.2:c.851-2766G>C
NM_001347701.2:c.*141C>G
NM_001347702.2:c.2864C>G
NM_033071.5:c.26186C>G
NM_182961.4:c.26330C>GMANE SELECT
NP_001334631.1:p.Ser955Cys
NP_149062.1:p.Ser8729Cys
NP_149062.2:p.Ser8729Cys
NP_892006.3:p.Ser8777Cys
LRG_427t1:c.26330C>G
LRG_427t2:c.26186C>G
LRG_427:g.519900C>G
LRG_427p1:p.Ser8777Cys
LRG_427p2:p.Ser8729Cys
LRG_992:g.470810G>C
NC_000006.11:g.152443635G>C
NM_033071.3:c.26186C>G
NM_182961.2:c.26330C>G

Protein change:

S8729C

Links:

dbSNP: rs377446250

NCBI 1000 Genomes Browser:

rs377446250

Molecular consequence:

NM_001347701.2:c.*141C>G - 3 prime UTR variant - [Sequence Ontology: SO:0001624]
NM_001328100.2:c.851-2766G>C - intron variant - [Sequence Ontology: SO:0001627]
NM_001347702.2:c.2864C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_033071.5:c.26186C>G - missense variant - [Sequence Ontology: SO:0001583]
NM_182961.4:c.26330C>G - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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multifunctional methyltransferase subunit TRM112-like protein isoform 1 [Homo sa...
multifunctional methyltransferase subunit TRM112-like protein isoform 1 [Homo sapiens]
gi|7705477|ref|NP_057488.1|

Protein
Mus musculus tubulin cofactor A, mRNA (cDNA clone MGC:62914 IMAGE:1430777), comp...
Mus musculus tubulin cofactor A, mRNA (cDNA clone MGC:62914 IMAGE:1430777), complete cds
gi|30185786|gb|BC051475.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV000615652	Athena Diagnostics	criteria provided, single submitter (Athena Diagnostics Criteria)	Uncertain significance (May 14, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV000708893	Eurofins Ntd Llc (ga)	criteria provided, single submitter (EGL Classification Definitions 2015)	Uncertain significance (May 25, 2017)	germline	clinical testing	Citation Link,
SCV003824616	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Oct 5, 2020)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004012602	GeneDx	criteria provided, single submitter (GeneDx Variant Classification Process June 2021)	Uncertain significance (Jan 6, 2023)	germline	clinical testing	Citation Link,
SCV004701441	CeGaT Center for Human Genetics Tuebingen	criteria provided, single submitter (CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)	Uncertain significance (Feb 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	1	not provided	not provided	not provided	not provided	clinical testing
not provided	germline	unknown	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

A Standardized DNA Variant Scoring System for Pathogenicity Assessments in Mendelian Disorders.

Karbassi I, Maston GA, Love A, DiVincenzo C, Braastad CD, Elzinga CD, Bright AR, Previte D, Zhang K, Rowland CM, McCarthy M, Lapierre JL, Dubois F, Medeiros KA, Batish SD, Jones J, Liaquat K, Hoffman CA, Jaremko M, Wang Z, Sun W, Buller-Burckle A, et al.

Hum Mutat. 2016 Jan;37(1):127-34. doi: 10.1002/humu.22918. Epub 2015 Oct 29.

PubMed [citation]

PMID:: 26467025
PMCID:: PMC4737317

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 Athena Diagnostics, SCV000615652.2

#	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 Eurofins Ntd Llc (ga), SCV000708893.2

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

#	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		1	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV003824616.2

#	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, SCV004012602.1

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

Description

In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge

#	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, SCV004701441.8

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

Description

SYNE1: PM2

#	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		1	not provided	not provided	not provided

Last Updated: Nov 3, 2024

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