VCV002433727.2 - ClinVar

NM_002397.5(MEF2C):c.1207A>T (p.Thr403Ser)

Germline

Classification

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)

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

criteria provided, single submitter

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_002397.5(MEF2C):c.1207A>T (p.Thr403Ser)

Variation ID: 2433727 Accession: VCV002433727.2

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 5q14.3 5: 88722819 (GRCh38) [ NCBI UCSC ] 5: 88018636 (GRCh37) [ NCBI UCSC ]

Timeline in ClinVar

	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	Mar 5, 2023	Feb 4, 2024	Jun 18, 2020

HGVS

Nucleotide	Protein	Molecular consequence
NM_002397.5:c.1207A>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_002388.2:p.Thr403Ser	missense
NM_001131005.2:c.1177A>T	NP_001124477.1:p.Thr393Ser	missense
NM_001193347.1:c.1237A>T	NP_001180276.1:p.Thr413Ser	missense
NM_001193348.1:c.1039A>T	NP_001180277.1:p.Thr347Ser	missense
NM_001193349.3:c.967A>T	NP_001180278.1:p.Thr323Ser	missense
NM_001193350.2:c.1207A>T	NP_001180279.1:p.Thr403Ser	missense
NM_001308002.3:c.1183A>T	NP_001294931.1:p.Thr395Ser	missense
NM_001363581.2:c.1111A>T	NP_001350510.1:p.Thr371Ser	missense
NM_001364329.2:c.1207A>T	NP_001351258.1:p.Thr403Ser	missense
NM_001364330.2:c.1207A>T	NP_001351259.1:p.Thr403Ser	missense
NM_001364331.2:c.1207A>T	NP_001351260.1:p.Thr403Ser	missense
NM_001364332.2:c.967A>T	NP_001351261.1:p.Thr323Ser	missense
NM_001364333.2:c.1183A>T	NP_001351262.1:p.Thr395Ser	missense
NM_001364334.2:c.1111A>T	NP_001351263.1:p.Thr371Ser	missense
NM_001364335.2:c.1111A>T	NP_001351264.1:p.Thr371Ser	missense
NM_001364336.2:c.1111A>T	NP_001351265.1:p.Thr371Ser	missense
NM_001364337.2:c.1111A>T	NP_001351266.1:p.Thr371Ser	missense
NM_001364338.2:c.1141A>T	NP_001351267.1:p.Thr381Ser	missense
NM_001364339.2:c.1087A>T	NP_001351268.1:p.Thr363Ser	missense
NM_001364340.2:c.1087A>T	NP_001351269.1:p.Thr363Ser	missense
NM_001364341.2:c.1087A>T	NP_001351270.1:p.Thr363Ser	missense
NM_001364342.2:c.1087A>T	NP_001351271.1:p.Thr363Ser	missense
NM_001364343.2:c.1081A>T	NP_001351272.1:p.Thr361Ser	missense
NM_001364344.2:c.1063A>T	NP_001351273.1:p.Thr355Ser	missense
NM_001364345.2:c.1109A>T	NP_001351274.1:p.His370Leu	missense
NM_001364346.2:c.1109A>T	NP_001351275.1:p.His370Leu	missense
NM_001364347.2:c.1109A>T	NP_001351276.1:p.His370Leu	missense
NM_001364348.2:c.1085A>T	NP_001351277.1:p.His362Leu	missense
NM_001364349.2:c.1085A>T	NP_001351278.1:p.His362Leu	missense
NM_001364350.2:c.1085A>T	NP_001351279.1:p.His362Leu	missense
NM_001364352.2:c.1079A>T	NP_001351281.1:p.His360Leu	missense
NM_001364353.2:c.829A>T	NP_001351282.1:p.Thr277Ser	missense
NM_001364354.2:c.965A>T	NP_001351283.1:p.His322Leu	missense
NM_001364355.2:c.965A>T	NP_001351284.1:p.His322Leu	missense
NM_001364356.2:c.733A>T	NP_001351285.1:p.Thr245Ser	missense
NM_001364357.2:c.661A>T	NP_001351286.1:p.Thr221Ser	missense
NR_146284.1:n.451T>A		non-coding transcript variant
NC_000005.10:g.88722819T>A
NC_000005.9:g.88018636T>A
NG_023427.1:g.186287A>T

... more HGVS ... less HGVS

Protein change

H322L, H360L, H362L, H370L, T221S, T245S, T277S, T323S, T347S, T355S, T361S, T363S, T371S, T381S, T393S, T395S, T403S, T413S

Other names

Canonical SPDI

NC_000005.10:88722818:T:A

Functional consequence Help The effect of the variant on RNA or protein function, based on experimental evidence from submitters.

Global minor allele frequency (GMAF) Help The 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.

Allele frequency Help The frequency of the allele represented by this VCV record.

Links

VarSome

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
Gene	OMIM	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.
MEF2C		Sufficient evidence for dosage pathogenicity	Little evidence for dosage pathogenicity	GRCh38 GRCh37	465	576
MEF2C-AS2	-	-	-	GRCh38	-	84

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.
Intellectual disability, autosomal dominant 20	Uncertain significance (1)	criteria provided, single submitter	Jun 18, 2020	RCV003131581.3

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.
Uncertain significance (Jun 18, 2020)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Intellectual disability, autosomal dominant 20 Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV003810930.2 First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024

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.

Citations for germline classification of this variant

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 this variant ...

Record last updated Sep 17, 2024

ClinVar Genomic variation as it relates to human health

NM_002397.5(MEF2C):c.1207A>T (p.Thr403Ser)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...