rs104893990
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_001024630.4(RUNX2):c.572G>A(p.Ser191Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S191G) has been classified as Likely pathogenic.
Frequency
Consequence
NM_001024630.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RUNX2 | NM_001024630.4 | c.572G>A | p.Ser191Asn | missense_variant | 4/9 | ENST00000647337.2 | |
RUNX2 | NM_001369405.1 | c.530G>A | p.Ser177Asn | missense_variant | 2/7 | ||
RUNX2 | NM_001015051.4 | c.572G>A | p.Ser191Asn | missense_variant | 4/8 | ||
RUNX2 | NM_001278478.2 | c.530G>A | p.Ser177Asn | missense_variant | 2/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RUNX2 | ENST00000647337.2 | c.572G>A | p.Ser191Asn | missense_variant | 4/9 | NM_001024630.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 32
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Cleidocranial dysostosis Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Jul 01, 1997 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at