NM_001024630.4(RUNX2):c.246_260dup (p.Ala85_Ala89dup) AND not provided

Germline classification:: Uncertain significance (1 submission)
Last evaluated:: Dec 9, 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:: RCV001888596.6

Allele description [Variation Report for NM_001024630.4(RUNX2):c.246_260dup (p.Ala85_Ala89dup)]

NM_001024630.4(RUNX2):c.246_260dup (p.Ala85_Ala89dup)

Genes:

RUNX2:RUNX family transcription factor 2 [Gene - OMIM - HGNC]
LOC109611589:runt related transcription factor 2 polyalanine expansion region [Gene]

Variant type:

Duplication

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_001024630.4(RUNX2):c.246_260dup (p.Ala85_Ala89dup)

HGVS:

NC_000006.12:g.45422780_45422794dup
NG_008020.2:g.99464_99478dup
NG_052657.1:g.202_216dup
NM_001015051.4:c.246_260dup
NM_001024630.4:c.246_260dupMANE SELECT
NM_001278478.2:c.204_218dup
NM_001369405.1:c.204_218dup
NP_001015051.3:p.Ala85_Ala89dup
NP_001019801.3:p.Ala85_Ala89dup
NP_001265407.1:p.Ala71_Ala75dup
NP_001356334.1:p.Ala71_Ala75dup
NC_000006.11:g.45390505_45390506insGCGGCGGCGGCGGCT
NC_000006.11:g.45390517_45390531dup

Links:

dbSNP: rs758081485

NCBI 1000 Genomes Browser:

rs758081485

Molecular consequence:

NM_001015051.4:c.246_260dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001024630.4:c.246_260dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001278478.2:c.204_218dup - inframe_insertion - [Sequence Ontology: SO:0001821]
NM_001369405.1:c.204_218dup - inframe_insertion - [Sequence Ontology: SO:0001821]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

Recent activity

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gi|2639990509|gb|OR160033.1|

Nucleotide
poly [ADP-ribose] polymerase tankyrase-1 [Homo sapiens]
poly [ADP-ribose] polymerase tankyrase-1 [Homo sapiens]
gi|87239981|ref|NP_003738.2|

Protein

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV002139622	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Uncertain significance (Dec 9, 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

SCV002139622

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Uncertain significance
(Dec 9, 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, SCV002139622.3

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

Description

This variant, c.246_260dup, results in the insertion of 5 amino acid(s) of the RUNX2 protein (p.Ala85_Ala89dup), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with RUNX2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1377609). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. 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.

#	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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