rs104893991

Positions:

• chr6-45438040-G-A
• chr6-45438040-G-T

Variant summary

Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1 PM2 PM5 PP3_Moderate PP5_Very_Strong

The NM_001024630.4(RUNX2):​c.674G>A​(p.Arg225Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,452,666 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R225L) has been classified as Likely pathogenic.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000014 (0 hom.)
• Consequence: RUNX2 NM_001024630.4 missense
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:11 O:1
• Conservation: PhyloP100: 8.15

Genes affected

RUNX2 (HGNC:10472): (RUNX family transcription factor 2) This gene is a member of the RUNX family of transcription factors and encodes a nuclear protein with an Runt DNA-binding domain. This protein is essential for osteoblastic differentiation and skeletal morphogenesis and acts as a scaffold for nucleic acids and regulatory factors involved in skeletal gene expression. The protein can bind DNA both as a monomer or, with more affinity, as a subunit of a heterodimeric complex. Two regions of potential trinucleotide repeat expansions are present in the N-terminal region of the encoded protein, and these and other mutations in this gene have been associated with the bone development disorder cleidocranial dysplasia (CCD). Transcript variants that encode different protein isoforms result from the use of alternate promoters as well as alternate splicing. [provided by RefSeq, Jul 2016]

ACMG classification

Verdict is Pathogenic. Variant got 16 ACMG points.

• PM1: In a domain Runt (size 128) in uniprot entity RUNX2_HUMAN there are 37 pathogenic changes around while only 0 benign (100%) in NM_001024630.4
• PM2: Very rare variant in population databases, with high coverage
• PM5: Other missense variant is known to change same aminoacid residue: Variant chrnull-null-null-null is described in UniProt as null.
• PP3: MetaRNN computational evidence supports a deleterious effect, 0.907
• PP5: Variant 6-45438040-G-A is Pathogenic according to our data. Variant chr6-45438040-G-A is described in ClinVar as [Pathogenic]. Clinvar id is 9302.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr6-45438040-G-A is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RUNX2	NM_001024630.4	c.674G>A	p.Arg225Gln	missense_variant	5/9	ENST00000647337.2	NP_001019801.3
RUNX2	NM_001369405.1	c.632G>A	p.Arg211Gln	missense_variant	3/7		NP_001356334.1
RUNX2	NM_001015051.4	c.674G>A	p.Arg225Gln	missense_variant	5/8		NP_001015051.3
RUNX2	NM_001278478.2	c.632G>A	p.Arg211Gln	missense_variant	3/6		NP_001265407.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
RUNX2	ENST00000647337.2	c.674G>A	p.Arg225Gln	missense_variant	5/9		NM_001024630.4	ENSP00000495497.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000138 AC: 2 AN: 1452666 Hom.: 0 Cov.: 28 AF XY: 0.00000138 AC XY: 1 AN XY: 723354

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000181

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 32

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:11 Other:1

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Pathogenic:6

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Oct 12, 2023	Published functional studies demonstrate a damaging effect (Zhou et al., 1999; Morrison et al., 2012); Not observed in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 24634175, 10545612, 15301373, 29087131, 28056872, 24222232, 28898321, 10521292, 32381727, 33502061, 30506733, 35169780, 22912713) -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Feb 15, 2018	- -
Pathogenic, no assertion criteria provided	clinical testing	Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Labcorp Genetics (formerly Invitae), Labcorp	Dec 09, 2023	This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 225 of the RUNX2 protein (p.Arg225Gln). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with clinical features of cleidocranial dysplasia (PMID: 10545612, 24222232, 24634175). In at least one individual the variant was observed to be de novo. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 9302). 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 expected to disrupt RUNX2 protein function with a positive predictive value of 80%. Experimental studies have shown that this missense change affects RUNX2 function (PMID: 10545612). For these reasons, this variant has been classified as Pathogenic. -
Pathogenic, no assertion criteria provided	clinical testing	Genome Diagnostics Laboratory, University Medical Center Utrecht	-	- -
Pathogenic, criteria provided, single submitter	clinical testing	Clinical Genetics Laboratory, Skane University Hospital Lund	Jul 13, 2022	- -

Cleidocranial dysostosis Pathogenic:3 Other:1

Pathogenic, criteria provided, single submitter	clinical testing	Victorian Clinical Genetics Services, Murdoch Childrens Research Institute	May 25, 2020	Based on the classification scheme VCGS_Germline_v1.1.1, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss-of-function is a known mechanism of disease for this gene. Missense variants have been shown to reduce transactivation activities in this gene (PMID: 28505335, 19767586). (N) 0107 - This gene is known to be associated with autosomal dominant disease. (N) 0200 - Variant is predicted to result in a missense amino acid change from an arginine to a glutamine (exon 5). (N) 0251 - Variant is heterozygous. (N) 0301 - Variant is absent from gnomAD. (P) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (P) 0600 - Variant is located in an annotated domain or motif (Runt domain). (N) 0801 - Very strong previous evidence of pathogenicity in unrelated individuals. This variant has been reported in multiple families with cleidocranial dysplasia (ClinVar, PMID: 28056872, 28505335, 22023169). (P) 1208 - Inheritance information for this variant is not currently available. (N) Legend: (P) - Pathogenic, (N) - Neutral, (B) - Benign -
not provided, no classification provided	literature only	GeneReviews	-	- -
Pathogenic, no assertion criteria provided	literature only	OMIM	Nov 01, 1999	- -
Pathogenic, criteria provided, single submitter	clinical testing	Center of Excellence in Genomics and Precision Dentistry, Faculty of Dentistry, Chulalongkorn University	-	A de novo heterozygous missense variant c.674G>A, p.Arg225Gln in the RUNX2 gene was identified in a boy with CCD but not his unaffected parents by trio-WES analysis. This variant has been previously reported in patients with autosomal dominant cleidocranial dysplasia (OMIM 119600, Genet Mol Res. 2013 Oct 15;12(4):4567-74. PMID: 24222232) and classified as pathogenic by ACMG guidelines. -

RUNX2-related disorder Pathogenic:1

Pathogenic, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Feb 20, 2024

The RUNX2 c.674G>A variant is predicted to result in the amino acid substitution p.Arg225Gln. This variant has been reported to be pathogenic for cleidocranial dysplasia (Zhou et al. 1999. PubMed ID: 10545612; Lee et al. 2013. PubMed ID: 24222232; Wu et al. 2014. PubMed ID: 24634175). This variant was also reported in two CCD patients (father and daughter) who also had a limb-girdle myopathy phenotype (Hsueh et al. 2017. PubMed ID: 28056872). In addition, similar variants affecting the same amino acid (c.673C>T, p.Arg225Trp and c.674G>T, p.Arg225Leu) were also reported to be pathogenic (Quack et al. 1999. PubMed ID: 10521292; Zhang et al. 2009. PubMed ID: 19767586). Therefore, we classify this variant as pathogenic. -

Cleidocranial dysostosis;C3549874:Metaphyseal dysplasia-maxillary hypoplasia-brachydacty syndrome Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Fulgent Genetics, Fulgent Genetics

Feb 18, 2022

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Pathogenic	1.0
BayesDel_addAF	Pathogenic	0.47	D
BayesDel_noAF	Pathogenic	0.43
CADD	Pathogenic	30
DANN	Uncertain	1.0
DEOGEN2	Pathogenic	0.99	.;D;D;D;.;D;.;D
Eigen	Pathogenic	0.70
Eigen_PC	Pathogenic	0.67
FATHMM_MKL	Pathogenic	0.99	D
LIST_S2	Pathogenic	1.0	D;.;.;D;.;D;D;D
M_CAP	Pathogenic	0.52	D
MetaRNN	Pathogenic	0.91	D;D;D;D;D;D;D;D
MetaSVM	Pathogenic	1.0	D
MutationAssessor	Uncertain	2.9	M;M;M;M;M;.;.;.
PrimateAI	Pathogenic	0.85	D
PROVEAN	Uncertain	-3.9	.;D;.;D;D;.;D;.
REVEL	Pathogenic	0.90
Sift	Benign	0.032	.;D;.;D;D;.;D;.
Sift4G	Uncertain	0.054	T;T;.;T;T;T;T;T
Polyphen		0.95, 1.0	.;P;P;P;.;.;D;.
Vest4		0.81
MVP		0.98
MPC		0.78
ClinPred		0.99	D
GERP RS		4.6
Varity_R		0.74
gMVP		0.96

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs104893991; hg19: chr6-45405777;