NM_003151.4(STAT4):c.2064G>C (p.Arg688Ser) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Feb 20, 2022
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:: RCV002675565.3

Allele description [Variation Report for NM_003151.4(STAT4):c.2064G>C (p.Arg688Ser)]

NM_003151.4(STAT4):c.2064G>C (p.Arg688Ser)

Genes:

STAT4-AS1:STAT4 antisense RNA 1 [Gene - HGNC]
STAT4:signal transducer and activator of transcription 4 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

2q32.2

Genomic location:

Preferred name:

NM_003151.4(STAT4):c.2064G>C (p.Arg688Ser)

HGVS:

NC_000002.12:g.191031497C>G
NG_012852.1:g.124703G>C
NG_012852.2:g.219678G>C
NM_001243835.2:c.2064G>C
NM_003151.4:c.2064G>CMANE SELECT
NP_001230764.1:p.Arg688Ser
NP_003142.1:p.Arg688Ser
NC_000002.11:g.191896223C>G

Protein change:

R688S

Molecular consequence:

NM_001243835.2:c.2064G>C - missense variant - [Sequence Ontology: SO:0001583]
NM_003151.4:c.2064G>C - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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Homo sapiens OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66728411-6672...
Homo sapiens OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:66728411-66728992 (LOC127887729) on chromosome 17
gi|2391412352|ref|NG_137362.1|

Nucleotide
PREDICTED: Rattus norvegicus cyclin A1 (Ccna1), transcript variant X14, mRNA
PREDICTED: Rattus norvegicus cyclin A1 (Ccna1), transcript variant X14, mRNA
gi|2678917606|ref|XM_063281582.1|

Nucleotide
RecName: Full=Monocyte to macrophage differentiation factor 2; AltName: Full=Pro...
RecName: Full=Monocyte to macrophage differentiation factor 2; AltName: Full=Progestin and adipoQ receptor family member 10; AltName: Full=Progestin and adipoQ receptor family member X
gi|51701815|sp|Q8R189.1|PAQRA_MOUSE

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002985574	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Feb 20, 2022)	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

SCV002985574

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Feb 20, 2022)

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	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. doi: 10.1038/s41436-019-0624-9.

PubMed [citation]

PMID:: 28492532
PMCID:: PMC5632818

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV002985574.2

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

Description

Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. This variant has not been reported in the literature in individuals affected with STAT4-related conditions. This variant is present in population databases (rs768045385, gnomAD 0.05%). This sequence change replaces arginine, which is basic and polar, with serine, which is neutral and polar, at codon 688 of the STAT4 protein (p.Arg688Ser).

#	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

Last Updated: Sep 29, 2024

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