VCV002437158.4 - ClinVar

NM_012470.4(TNPO3):c.1249A>G (p.Met417Val)

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.

(2)

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, multiple submitters, no conflicts

Somatic

No data submitted for somatic clinical impact

Somatic

No data submitted for oncogenicity

Variant Details

Identifiers

NM_012470.4(TNPO3):c.1249A>G (p.Met417Val)

Variation ID: 2437158 Accession: VCV002437158.4

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 7q32.1 7: 128993824 (GRCh38) [ NCBI UCSC ] 7: 128633878 (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	May 1, 2024	Jul 25, 2023

HGVS

Nucleotide	Protein	Molecular consequence
NM_012470.4:c.1249A>G MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_036602.1:p.Met417Val	missense
NM_001191028.3:c.1249A>G	NP_001177957.2:p.Met417Val	missense
NM_001382216.1:c.1249A>G	NP_001369145.1:p.Met417Val	missense
NM_001382217.1:c.1330A>G	NP_001369146.1:p.Met444Val	missense
NM_001382218.1:c.1249A>G	NP_001369147.1:p.Met417Val	missense
NM_001382219.1:c.1159-1734A>G		intron variant
NM_001382220.1:c.1249A>G	NP_001369149.1:p.Met417Val	missense
NM_001382221.1:c.1105A>G	NP_001369150.1:p.Met369Val	missense
NM_001382222.1:c.1102A>G	NP_001369151.1:p.Met368Val	missense
NM_001382223.1:c.1249A>G	NP_001369152.1:p.Met417Val	missense
NR_034053.3:n.1751A>G		non-coding transcript variant
NR_167911.1:n.1838A>G		non-coding transcript variant
NR_167912.1:n.1590A>G		non-coding transcript variant
NR_167913.1:n.1590A>G		non-coding transcript variant
NR_167914.1:n.1658A>G		non-coding transcript variant
NR_167915.1:n.1751A>G		non-coding transcript variant
NR_167916.1:n.1590A>G		non-coding transcript variant
NR_167917.1:n.1590A>G		non-coding transcript variant
NR_167918.1:n.1876A>G		non-coding transcript variant
NR_167919.1:n.1715A>G		non-coding transcript variant
NR_167920.1:n.1876A>G		non-coding transcript variant
NR_167921.1:n.1876A>G		non-coding transcript variant
NR_167922.1:n.1712A>G		non-coding transcript variant
NR_167923.1:n.1715A>G		non-coding transcript variant
NR_167924.1:n.1590A>G		non-coding transcript variant
NR_167925.1:n.1590A>G		non-coding transcript variant
NR_167926.1:n.1726A>G		non-coding transcript variant
NR_167927.1:n.1715A>G		non-coding transcript variant
NC_000007.14:g.128993824T>C
NC_000007.13:g.128633878T>C
NG_023428.1:g.66350A>G

... more HGVS ... less HGVS

Protein change

M368V, M369V, M417V, M444V

Other names

Canonical SPDI

NC_000007.14:128993823:T:C

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.
TNPO3		-	-	GRCh38 GRCh37	620	680

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.
Autosomal dominant limb-girdle muscular dystrophy type 1F	Uncertain significance (1)	criteria provided, single submitter	Apr 1, 2019	RCV003141078.3
Inborn genetic diseases	Uncertain significance (1)	criteria provided, single submitter	Jul 25, 2023	RCV003377932.2

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 (Apr 01, 2019)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	Autosomal dominant limb-girdle muscular dystrophy type 1F Affected status: unknown Allele origin: germline	Revvity Omics, Revvity Accession: SCV003827760.2 First in ClinVar: Mar 04, 2023 Last updated: Feb 04, 2024
Uncertain significance (Jul 25, 2023)	criteria provided, single submitter (Ambry Variant Classification Scheme 2023) Method: clinical testing	Inborn genetic diseases Affected status: unknown Allele origin: germline	Ambry Genetics Accession: SCV004086711.2 First in ClinVar: Oct 28, 2023 Last updated: May 01, 2024	Comment: The c.1249A>G (p.M417V) alteration is located in exon 9 (coding exon 9) of the TNPO3 gene. This alteration results from a A to G substitution … (more) The c.1249A>G (p.M417V) alteration is located in exon 9 (coding exon 9) of the TNPO3 gene. This alteration results from a A to G substitution at nucleotide position 1249, causing the methionine (M) at amino acid position 417 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. (less)

Comment:

The c.1249A>G (p.M417V) alteration is located in exon 9 (coding exon 9) of the TNPO3 gene. This alteration results from a A to G substitution at nucleotide position 1249, causing the methionine (M) at amino acid position 417 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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:

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 May 01, 2024

ClinVar Genomic variation as it relates to human health

NM_012470.4(TNPO3):c.1249A>G (p.Met417Val)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for this variant ...