NM_001366145.2(TRPM3):c.4404C>A (p.Ser1468Arg) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 25, 2020
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:: RCV001864870.6

Allele description [Variation Report for NM_001366145.2(TRPM3):c.4404C>A (p.Ser1468Arg)]

NM_001366145.2(TRPM3):c.4404C>A (p.Ser1468Arg)

Genes:

KLF9-DT:KLF9 divergent transcript [Gene - HGNC]
TRPM3:transient receptor potential cation channel subfamily M member 3 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

9q21.12

Genomic location:

Preferred name:

NM_001366145.2(TRPM3):c.4404C>A (p.Ser1468Arg)

HGVS:

NC_000009.12:g.70536709G>T
NG_047197.1:g.915216C>A
NM_001007471.4:c.4368C>A
NM_001366141.2:c.4374C>A
NM_001366142.2:c.3997+413C>A
NM_001366143.2:c.3961+413C>A
NM_001366145.2:c.4404C>AMANE SELECT
NM_001366146.2:c.3991+413C>A
NM_001366147.2:c.4479C>A
NM_001366148.2:c.4036+413C>A
NM_001366149.2:c.4374C>A
NM_001366150.2:c.3925+413C>A
NM_001366151.2:c.3955+413C>A
NM_001366152.2:c.4066+413C>A
NM_001366154.2:c.3532+413C>A
NM_020952.6:c.3909C>A
NM_024971.7:c.3945C>A
NM_206944.5:c.3879C>A
NM_206945.5:c.3915C>A
NM_206946.5:c.3984C>A
NM_206947.5:c.3954C>A
NP_001007472.2:p.Ser1456Arg
NP_001353070.1:p.Ser1458Arg
NP_001353074.1:p.Ser1468Arg
NP_001353076.1:p.Ser1493Arg
NP_001353078.1:p.Ser1458Arg
NP_066003.3:p.Ser1303Arg
NP_079247.5:p.Ser1315Arg
NP_996827.3:p.Ser1293Arg
NP_996828.3:p.Ser1305Arg
NP_996829.3:p.Ser1328Arg
NP_996830.3:p.Ser1318Arg
NC_000009.11:g.73151625G>T

Protein change:

S1293R

Links:

dbSNP: rs763169990

NCBI 1000 Genomes Browser:

rs763169990

Molecular consequence:

NM_001366142.2:c.3997+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001366143.2:c.3961+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001366146.2:c.3991+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001366148.2:c.4036+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001366150.2:c.3925+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001366151.2:c.3955+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001366152.2:c.4066+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001366154.2:c.3532+413C>A - intron variant - [Sequence Ontology: SO:0001627]
NM_001007471.4:c.4368C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001366141.2:c.4374C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001366145.2:c.4404C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001366147.2:c.4479C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_001366149.2:c.4374C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_020952.6:c.3909C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_024971.7:c.3945C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_206944.5:c.3879C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_206945.5:c.3915C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_206946.5:c.3984C>A - missense variant - [Sequence Ontology: SO:0001583]
NM_206947.5:c.3954C>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2 isoform X...
arf-GAP with SH3 domain, ANK repeat and PH domain-containing protein 2 isoform X14 [Homo sapiens]
gi|2462578188|ref|XP_054200363.1|

Protein
PREDICTED: Homo sapiens ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 (...
PREDICTED: Homo sapiens ArfGAP with SH3 domain, ankyrin repeat and PH domain 2 (ASAP2), transcript variant X18, mRNA
gi|2462578195|ref|XM_054344392.1|

Nucleotide

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002124643	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 25, 2020)	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

SCV002124643

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 25, 2020)

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, SCV002124643.3

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

Description

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 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: "Not Available"; Align-GVGD: "Class C0"). This variant has not been reported in the literature in individuals with TRPM3-related conditions. This variant is present in population databases (rs763169990, ExAC 0.004%). This sequence change replaces serine with arginine at codon 1303 of the TRPM3 protein (p.Ser1303Arg). The serine residue is moderately conserved and there is a moderate physicochemical difference between serine and arginine.

#	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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