NM_014112.5(TRPS1):c.2026A>G (p.Ser676Gly) AND multiple conditions

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Jan 10, 2023
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:: RCV003795116.2

Allele description [Variation Report for NM_014112.5(TRPS1):c.2026A>G (p.Ser676Gly)]

NM_014112.5(TRPS1):c.2026A>G (p.Ser676Gly)

Gene:

TRPS1:transcriptional repressor GATA binding 1 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

8q23.3

Genomic location:

Preferred name:

NM_014112.5(TRPS1):c.2026A>G (p.Ser676Gly)

HGVS:

NC_000008.11:g.115603943T>C
NG_012383.3:g.70059A>G
NM_001282902.3:c.1999A>G
NM_001282903.3:c.2005A>G
NM_001330599.2:c.1987A>G
NM_014112.5:c.2026A>GMANE SELECT
NP_001269831.1:p.Ser667Gly
NP_001269832.1:p.Ser669Gly
NP_001317528.1:p.Ser663Gly
NP_054831.2:p.Ser676Gly
NC_000008.10:g.116616170T>C

Protein change:

S663G

Molecular consequence:

NM_001282902.3:c.1999A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001282903.3:c.2005A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_001330599.2:c.1987A>G - missense variant - [Sequence Ontology: SO:0001583]
NM_014112.5:c.2026A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:: Trichorhinophalangeal syndrome, type III (TRPS3)
Synonyms:: Trichorhinophalangeal syndrome type 3; TRPS 3; Sugio-Kajii Syndrome
Identifiers:: MONDO: MONDO:0008597; MedGen: C1860823; Orphanet: 77258; OMIM: 190351

Name:: Trichorhinophalangeal dysplasia type I (TRPS1)
Synonyms:: TRPS I; Trichorhinophalangeal syndrome type 1; Giedion syndrome; See all synonyms [MedGen]
Identifiers:: MONDO: MONDO:0008596; MedGen: C0432233; Orphanet: 77258; OMIM: 190350

Recent activity

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SAMN16475162 (1)
SRA
maturase, partial (chloroplast) [Aegilops biuncialis]
maturase, partial (chloroplast) [Aegilops biuncialis]
gi|510381031|gb|AGN48068.1|

Protein
RecName: Full=Solute carrier family 22 member 17; AltName: Full=24p3 receptor; S...
RecName: Full=Solute carrier family 22 member 17; AltName: Full=24p3 receptor; Short=24p3R; AltName: Full=Brain-type organic cation transporter; AltName: Full=Lipocalin-2 receptor; AltName: Full=Neutrophil gelatinase-associated lipocalin receptor; Short=NgalR
gi|2664702668|sp|Q8WUG5.2|S22AH_HUM

Protein
Homo sapiens 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR), tran...
Homo sapiens 5-methyltetrahydrofolate-homocysteine methyltransferase (MTR), transcript variant 1, mRNA
gi|1844139169|ref|NM_000254.3|

Nucleotide
ataxin-7-like protein 2 isoform X1 [Homo sapiens]
ataxin-7-like protein 2 isoform X1 [Homo sapiens]
gi|767902267|ref|XP_011538940.1|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004590104	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Jan 10, 2023)	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

SCV004590104

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Jan 10, 2023)

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, SCV004590104.1

#	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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt TRPS1 protein function. This variant has not been reported in the literature in individuals affected with TRPS1-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with glycine, which is neutral and non-polar, at codon 676 of the TRPS1 protein (p.Ser676Gly).

#	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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