NM_001330677.2(TBX15):c.1325G>A (p.Arg442Lys) AND Pelviscapular dysplasia

Germline classification:: Conflicting interpretations of pathogenicity (2 submissions)
Last evaluated:: Oct 30, 2023
Review status:: criteria provided, conflicting classifications

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:: RCV001270113.3

Allele description [Variation Report for NM_001330677.2(TBX15):c.1325G>A (p.Arg442Lys)]

NM_001330677.2(TBX15):c.1325G>A (p.Arg442Lys)

Gene:

TBX15:T-box transcription factor 15 [Gene - OMIM - HGNC]

Variant type:

single nucleotide variant

Cytogenetic location:

1p12

Genomic location:

Preferred name:

NM_001330677.2(TBX15):c.1325G>A (p.Arg442Lys)

HGVS:

NC_000001.11:g.118885216C>T
NG_013361.1:g.109341G>A
NM_001330677.2:c.1325G>AMANE SELECT
NM_152380.2:c.1007G>A
NM_152380.3:c.1007G>A
NP_001317606.1:p.Arg442Lys
NP_689593.2:p.Arg336Lys
NC_000001.10:g.119427839C>T
NM_152380.3:c.1007G>A

Protein change:

R336K

Links:

dbSNP: rs144291418

NCBI 1000 Genomes Browser:

rs144291418

Molecular consequence:

NM_001330677.2:c.1325G>A - missense variant - [Sequence Ontology: SO:0001583]
NM_152380.3:c.1007G>A - missense variant - [Sequence Ontology: SO:0001583]

Observations:

Condition(s)

Name:: Pelviscapular dysplasia
Synonyms:: Cousin syndrome; Craniofacial dysmorphism, hypoplasia of scapula and pelvis and short stature
Identifiers:: MONDO: MONDO:0009845; MedGen: C1850040; Orphanet: 93333; OMIM: 260660

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV001448964	Knight Diagnostic Laboratories, Oregon Health and Sciences University	criteria provided, single submitter (ACMG Guidelines, 2015)	Uncertain significance (Mar 18, 2019)	germline	clinical testing	PubMed (1) [See all records that cite this PMID]
SCV004237883	Revvity Omics, Revvity	criteria provided, single submitter (ACMG Guidelines, 2015)	Likely benign (Oct 30, 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

SCV001448964

Knight Diagnostic Laboratories, Oregon Health and Sciences University

criteria provided, single submitter

(ACMG Guidelines, 2015)

Uncertain significance
(Mar 18, 2019)

germline

clinical testing

PubMed (1)
[See all records that cite this PMID]

SCV004237883

Revvity Omics, Revvity

criteria provided, single submitter

(ACMG Guidelines, 2015)

Likely benign
(Oct 30, 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	1	not provided	not provided	not provided	not provided	clinical testing

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]

PMID:: 25741868
PMCID:: PMC4544753

Details of each submission

From Knight Diagnostic Laboratories, Oregon Health and Sciences University, SCV001448964.1

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

#	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		1	not provided	not provided	not provided

From Revvity Omics, Revvity, SCV004237883.1

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

#	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: Oct 13, 2024

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