We classify this variant as a variant of uncertain significance using ACMG/AMP criteria. As this variant has been validated in an exome-wide approach, we suspect this variant is favoring pathogenic.
ClinVar Genomic variation as it relates to human health
NM_001083962.2(TCF4):c.562T>A (p.Ser188Thr)
Germline
Classification
Help
The aggregate germline classification for this variant, typically for a monogenic or Mendelian disorder as in the ACMG/AMP guidelines, or for response to a drug. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the aggregate classification.
(1)
Help
Stars represent the aggregate review status, or the level of review supporting the aggregate germline classification for this VCV record. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. The number of submissions which contribute to this review status is shown in parentheses.
Uncertain significance
1
criteria provided, single submitter
Somatic
No data submitted for somatic clinical impact
Somatic
No data submitted for oncogenicity
Variant Details
- Identifiers
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NM_001083962.2(TCF4):c.562T>A (p.Ser188Thr)
Variation ID: 1327136 Accession: VCV001327136.1
- Type and length
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single nucleotide variant, 1 bp
- Location
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Cytogenetic: 18q21.2 18: 55279644 (GRCh38) [ NCBI UCSC ] 18: 52946875 (GRCh37) [ NCBI UCSC ]
- Timeline in ClinVar
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First in ClinVar Help The date this variant first appeared in ClinVar with each type of classification.
Last submission Help The date of the most recent submission for each type of classification for this variant.
Last evaluated Help The most recent date that a submitter evaluated this variant for each type of classification.
Germline Dec 12, 2021 Dec 12, 2021 Oct 1, 2021 - HGVS
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... more HGVS ... less HGVSNucleotide Protein Molecular
consequenceNM_001083962.2:c.562T>A MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.
NP_001077431.1:p.Ser188Thr missense NM_001243226.3:c.868T>A NP_001230155.2:p.Ser290Thr missense NM_001243227.2:c.490T>A NP_001230156.1:p.Ser164Thr missense NM_001243228.2:c.580T>A NP_001230157.1:p.Ser194Thr missense NM_001243230.2:c.556T>A NP_001230159.1:p.Ser186Thr missense NM_001243231.2:c.436T>A NP_001230160.1:p.Ser146Thr missense NM_001243232.1:c.349T>A NP_001230161.1:p.Ser117Thr missense NM_001243233.2:c.172T>A NP_001230162.1:p.Ser58Thr missense NM_001243234.2:c.82T>A NP_001230163.1:p.Ser28Thr missense NM_001243235.2:c.82T>A NP_001230164.1:p.Ser28Thr missense NM_001243236.2:c.82T>A NP_001230165.1:p.Ser28Thr missense NM_001306207.1:c.490T>A NP_001293136.1:p.Ser164Thr missense NM_001306208.1:c.349T>A NP_001293137.1:p.Ser117Thr missense NM_001330604.3:c.562T>A NP_001317533.1:p.Ser188Thr missense NM_001330605.3:c.172T>A NP_001317534.1:p.Ser58Thr missense NM_001348211.2:c.436T>A NP_001335140.1:p.Ser146Thr missense NM_001348212.2:c.172T>A NP_001335141.1:p.Ser58Thr missense NM_001348213.2:c.172T>A NP_001335142.1:p.Ser58Thr missense NM_001348214.2:c.82T>A NP_001335143.1:p.Ser28Thr missense NM_001348215.2:c.-87T>A 5 prime UTR NM_001348216.2:c.82T>A NP_001335145.1:p.Ser28Thr missense NM_001348217.1:c.490T>A NP_001335146.1:p.Ser164Thr missense NM_001348218.2:c.490T>A NP_001335147.1:p.Ser164Thr missense NM_001348219.2:c.490T>A NP_001335148.1:p.Ser164Thr missense NM_001348220.1:c.487T>A NP_001335149.1:p.Ser163Thr missense NM_001369567.1:c.562T>A NP_001356496.1:p.Ser188Thr missense NM_001369568.1:c.562T>A NP_001356497.1:p.Ser188Thr missense NM_001369569.1:c.559T>A NP_001356498.1:p.Ser187Thr missense NM_001369570.1:c.559T>A NP_001356499.1:p.Ser187Thr missense NM_001369571.1:c.562T>A NP_001356500.1:p.Ser188Thr missense NM_001369572.1:c.562T>A NP_001356501.1:p.Ser188Thr missense NM_001369573.1:c.559T>A NP_001356502.1:p.Ser187Thr missense NM_001369574.1:c.562T>A NP_001356503.1:p.Ser188Thr missense NM_001369575.1:c.490T>A NP_001356504.1:p.Ser164Thr missense NM_001369576.1:c.487T>A NP_001356505.1:p.Ser163Thr missense NM_001369577.1:c.490T>A NP_001356506.1:p.Ser164Thr missense NM_001369578.1:c.487T>A NP_001356507.1:p.Ser163Thr missense NM_001369579.1:c.490T>A NP_001356508.1:p.Ser164Thr missense NM_001369580.1:c.490T>A NP_001356509.1:p.Ser164Thr missense NM_001369581.1:c.487T>A NP_001356510.1:p.Ser163Thr missense NM_001369582.1:c.490T>A NP_001356511.1:p.Ser164Thr missense NM_001369583.1:c.490T>A NP_001356512.1:p.Ser164Thr missense NM_001369584.1:c.487T>A NP_001356513.1:p.Ser163Thr missense NM_001369585.1:c.487T>A NP_001356514.1:p.Ser163Thr missense NM_001369586.1:c.490T>A NP_001356515.1:p.Ser164Thr missense NM_003199.3:c.562T>A NP_003190.1:p.Ser188Thr missense NC_000018.10:g.55279644A>T NC_000018.9:g.52946875A>T NG_011716.2:g.361350T>A - Protein change
- S117T, S146T, S163T, S164T, S186T, S187T, S188T, S194T, S28T, S290T, S58T
- Other names
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- Canonical SPDI
- NC_000018.10:55279643:A:T
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Functional
consequence HelpThe effect of the variant on RNA or protein function, based on experimental evidence from submitters.
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Global minor allele
frequency (GMAF) HelpThe global minor allele frequency calculated by the 1000 Genomes Project. The minor allele at this location is indicated in parentheses and may be different from the allele represented by this VCV record.
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Allele frequency
Help
The frequency of the allele represented by this VCV record.
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- Links
Genes
| Gene | OMIM | ClinGen Gene Dosage Sensitivity Curation |
Variation Viewer
Help
Links to Variation Viewer, a genome browser to view variation data from NCBI databases. |
Related variants | ||
|---|---|---|---|---|---|---|
| HI score
Help
The haploinsufficiency score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
TS score
Help
The triplosensitivity score for the gene, curated by ClinGen’s Dosage Sensitivity Curation task team. |
Within gene
Help
The number of variants in ClinVar that are contained within this gene, with a link to view the list of variants. |
All
Help
The number of variants in ClinVar for this gene, including smaller variants within the gene and larger CNVs that overlap or fully contain the gene. |
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| TCF4 | Sufficient evidence for dosage pathogenicity | No evidence available |
GRCh38 GRCh37 |
993 | 1220 | |
Conditions - Germline
| Condition
Help
The condition for this variant-condition (RCV) record in ClinVar. |
Classification
Help
The aggregate germline classification for this variant-condition (RCV) record in ClinVar. The number of submissions that contribute to this aggregate classification is shown in parentheses. (# of submissions) |
Review status
Help
The aggregate review status for this variant-condition (RCV) record in ClinVar. This value is calculated by NCBI based on data from submitters. Read our rules for calculating the review status. |
Last evaluated
Help
The most recent date that a submitter evaluated this variant for the condition. |
Variation/condition record
Help
The RCV accession number, with most recent version number, for the variant-condition record, with a link to the RCV web page. |
|---|---|---|---|---|
| Uncertain significance (1) |
criteria provided, single submitter
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Oct 1, 2021 | RCV001787419.1 |
Submissions - Germline
| Classification
Help
The submitted germline classification for each SCV record. (Last evaluated) |
Review status
Help
Stars represent the review status, or the level of review supporting the submitted (SCV) record. This value is calculated by NCBI based on data from the submitter. Read our rules for calculating the review status. This column also includes a link to the submitter’s assertion criteria if provided, and the collection method. (Assertion criteria) |
Condition
Help
The condition for the classification, provided by the submitter for this submitted (SCV) record. This column also includes the affected status and allele origin of individuals observed with this variant. |
Submitter
Help
The submitting organization for this submitted (SCV) record. This column also includes the SCV accession and version number, the date this SCV first appeared in ClinVar, and the date that this SCV was last updated in ClinVar. |
More information
Help
This column includes more information supporting the classification, including citations, the comment on classification, and detailed evidence provided as observations of the variant by the submitter. |
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Uncertain significance
(Oct 01, 2021)
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criteria provided, single submitter
Method: research
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SUDDEN INFANT DEATH SYNDROME
Affected status: yes
Allele origin:
germline
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Robert's Program, Boston Children's Hospital
Accession: SCV002030084.1
First in ClinVar: Dec 12, 2021 Last updated: Dec 12, 2021 |
Comment:
We classify this variant as a variant of uncertain significance using ACMG/AMP criteria. As this variant has been validated in an exome-wide approach, we suspect … (more)
We classify this variant as a variant of uncertain significance using ACMG/AMP criteria. As this variant has been validated in an exome-wide approach, we suspect this variant is favoring pathogenic. (less)
Clinical Features:
Sudden infant death syndrome (present)
Sex: male
|
Comment:
Germline Functional Evidence
| There is no functional evidence in ClinVar for this variation. If you have generated functional data for this variation, please consider submitting that data to ClinVar. |
Comment:
We classify this variant as a variant of uncertain significance using ACMG/AMP criteria. As this variant has been validated in an exome-wide approach, we suspect this variant is favoring pathogenic.
Citations for germline classification of this variant
Help| There are no citations for germline classification of this variant in ClinVar. If you know of citations for this variation, please consider submitting that information to ClinVar. |
Text-mined citations for rs2146265783 ...
HelpThese citations are identified by LitVar using
the rs number, so they may include citations for more than one variant
at this location. Please review the LitVar results carefully for your
variant of interest.
Record last updated May 19, 2024
This date represents the last time this VCV record was updated. The update may be due to an update to one of the included submitted records (SCVs), or due to an update that ClinVar made to the variant such as adding HGVS expressions or a rs number. So this date may be different from the date of the “most recent submission” reported at the top of this page.