VCV001333407.1 - ClinVar

NM_001366145.2(TRPM3):c.2234C>T (p.Ala745Val)

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_001366145.2(TRPM3):c.2234C>T (p.Ala745Val)

Variation ID: 1333407 Accession: VCV001333407.1

Type and length

single nucleotide variant, 1 bp

Location

Cytogenetic: 9q21.12 9: 70618991 (GRCh38) [ NCBI UCSC ] 9: 73233907 (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	Jan 15, 2022	Jan 15, 2022	Jan 3, 2022

HGVS

Nucleotide	Protein	Molecular consequence
NM_001366145.2:c.2234C>T MANE Select Help Transcripts from the Matched Annotation from the NCBI and EMBL-EBI (MANE) collaboration.	NP_001353074.1:p.Ala745Val	missense
NM_001007471.4:c.2198C>T	NP_001007472.2:p.Ala733Val	missense
NM_001366141.2:c.2204C>T	NP_001353070.1:p.Ala735Val	missense
NM_001366142.2:c.2240C>T	NP_001353071.1:p.Ala747Val	missense
NM_001366143.2:c.2204C>T	NP_001353072.1:p.Ala735Val	missense
NM_001366146.2:c.2234C>T	NP_001353075.1:p.Ala745Val	missense
NM_001366147.2:c.2309C>T	NP_001353076.1:p.Ala770Val	missense
NM_001366148.2:c.2279C>T	NP_001353077.1:p.Ala760Val	missense
NM_001366149.2:c.2204C>T	NP_001353078.1:p.Ala735Val	missense
NM_001366150.2:c.2168C>T	NP_001353079.1:p.Ala723Val	missense
NM_001366151.2:c.2198C>T	NP_001353080.1:p.Ala733Val	missense
NM_001366152.2:c.2309C>T	NP_001353081.1:p.Ala770Val	missense
NM_001366154.2:c.1775C>T	NP_001353083.1:p.Ala592Val	missense
NM_020952.6:c.1739C>T	NP_066003.3:p.Ala580Val	missense
NM_024971.7:c.1775C>T	NP_079247.5:p.Ala592Val	missense
NM_206944.5:c.1709C>T	NP_996827.3:p.Ala570Val	missense
NM_206945.5:c.1745C>T	NP_996828.3:p.Ala582Val	missense
NM_206946.5:c.1814C>T	NP_996829.3:p.Ala605Val	missense
NM_206947.5:c.1784C>T	NP_996830.3:p.Ala595Val	missense
NC_000009.12:g.70618991G>A
NC_000009.11:g.73233907G>A
NG_047197.1:g.832934C>T

... more HGVS ... less HGVS

Protein change

A570V, A580V, A582V, A592V, A595V, A605V, A723V, A733V, A735V, A745V, A747V, A760V, A770V

Other names

Canonical SPDI

NC_000009.12:70618990:G: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

dbSNP: rs149734399 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.
TRPM3		-	-	GRCh38 GRCh37	158	307

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.
TRPM3 related neruodevelopmental disorder	Uncertain significance (1)	criteria provided, single submitter	Jan 3, 2022	RCV001808095.1

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.
Uncertain significance (Jan 03, 2022)	criteria provided, single submitter (ACMG Guidelines, 2015) Method: clinical testing	TRPM3 related neruodevelopmental disorder Affected status: yes Allele origin: germline	3billion Accession: SCV002058563.1 First in ClinVar: Jan 15, 2022 Last updated: Jan 15, 2022	Comment: The variant not observed in the gnomAD v2.1.1 dataset (PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product … (more) The variant not observed in the gnomAD v2.1.1 dataset (PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.813, PP3_P). A missense variant is a common mechanism associated with TRPM3-related intellectual disabilities with epilepsy (PP2_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline. (less) Clinical Features: Hyperopic astigmatism (present) , Intellectual disability (present) , Microcephaly (present) , Low hanging columella (present) , Short philtrum (present) , Strabismus (present) , Dystonic disorder … (more) Hyperopic astigmatism (present) , Intellectual disability (present) , Microcephaly (present) , Low hanging columella (present) , Short philtrum (present) , Strabismus (present) , Dystonic disorder (present) , CNS hypomyelination (present) (less)

Comment:

The variant not observed in the gnomAD v2.1.1 dataset (PM2_M). In silico tool predictions suggest damaging effect of the variant on gene or gene product (3CNET: 0.813, PP3_P). A missense variant is a common mechanism associated with TRPM3-related intellectual disabilities with epilepsy (PP2_P). Therefore, this variant is classified as uncertain significance according to the recommendation of ACMG/AMP guideline.

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 rs149734399 ...

These 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 Dec 25, 2023

ClinVar Genomic variation as it relates to human health

NM_001366145.2(TRPM3):c.2234C>T (p.Ala745Val)

Variant Details

Genes

Conditions - Germline

Submissions - Germline

Germline Functional Evidence

Citations for germline classification of this variant

Text-mined citations for rs149734399 ...