NM_001024630.4(RUNX2):c.196C>T (p.Gln66Ter) AND not provided

Germline classification:: Pathogenic (1 submission)
Last evaluated:: Dec 24, 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:: RCV003555262.2

Allele description [Variation Report for NM_001024630.4(RUNX2):c.196C>T (p.Gln66Ter)]

NM_001024630.4(RUNX2):c.196C>T (p.Gln66Ter)

Genes:

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

Variant type:

single nucleotide variant

Cytogenetic location:

6p21.1

Genomic location:

Preferred name:

NM_001024630.4(RUNX2):c.196C>T (p.Gln66Ter)

HGVS:

NC_000006.12:g.45422730C>T
NG_008020.2:g.99414C>T
NG_052657.1:g.152C>T
NM_001015051.4:c.196C>T
NM_001024630.4:c.196C>TMANE SELECT
NM_001278478.2:c.154C>T
NM_001369405.1:c.154C>T
NM_004348.3:c.154C>T
NP_001015051.3:p.Gln66Ter
NP_001019801.3:p.Gln66Ter
NP_001265407.1:p.Gln52Ter
NP_001356334.1:p.Gln52Ter
NP_004339.3:p.Gln52Ter
NC_000006.11:g.45390467C>T

Protein change:

Q52*

Molecular consequence:

NM_001015051.4:c.196C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001024630.4:c.196C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001278478.2:c.154C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_001369405.1:c.154C>T - nonsense - [Sequence Ontology: SO:0001587]
NM_004348.3:c.154C>T - nonsense - [Sequence Ontology: SO:0001587]

Condition(s)

Synonyms:: none provided
Identifiers:: MedGen: C3661900

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Submission Accession	Submitter	Review Status (Assertion method)	Clinical Significance (Last evaluated)	Origin	Method	Citations
SCV004293662	Labcorp Genetics (formerly Invitae), Labcorp	criteria provided, single submitter (Invitae Variant Classification Sherloc (09022015))	Pathogenic (Dec 24, 2023)	germline	clinical testing	PubMed (4) [See all records that cite these PMIDs] 10521292, 11857736, 35598271, 28492532

Submission Accession

Submitter

Review Status
(Assertion method)

Clinical Significance
(Last evaluated)

Origin

Method

Citations

SCV004293662

Labcorp Genetics (formerly Invitae), Labcorp

criteria provided, single submitter

(Invitae Variant Classification Sherloc (09022015))

Pathogenic
(Dec 24, 2023)

germline

clinical testing

PubMed (4)
[See all records that cite these PMIDs]

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

Mutation analysis of core binding factor A1 in patients with cleidocranial dysplasia.

Quack I, Vonderstrass B, Stock M, Aylsworth AS, Becker A, Brueton L, Lee PJ, Majewski F, Mulliken JB, Suri M, Zenker M, Mundlos S, Otto F.

Am J Hum Genet. 1999 Nov;65(5):1268-78.

PubMed [citation]

PMID:: 10521292
PMCID:: PMC1288279

Mutations in the RUNX2 gene in patients with cleidocranial dysplasia.

Otto F, Kanegane H, Mundlos S.

Hum Mutat. 2002 Mar;19(3):209-16. Review.

PubMed [citation]

PMID:: 11857736

See all PubMed Citations (4)

Details of each submission

From Labcorp Genetics (formerly Invitae), Labcorp, SCV004293662.1

#	Ethnicity	Individuals	Chromosomes Tested	Family History	Method	Citations
1	not provided	not provided	not provided	not provided	clinical testing	PubMed (4)

Description

This sequence change creates a premature translational stop signal (p.Gln66*) in the RUNX2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in RUNX2 are known to be pathogenic (PMID: 10521292, 11857736). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with cleidocranial dysplasia (PMID: 11857736, 35598271). For these reasons, this variant has been classified as Pathogenic.

#	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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