rs72659325
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP2PP3_StrongPP5
The NM_000089.4(COL1A2):c.3106G>C(p.Gly1036Arg) variant causes a missense, splice region 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. 14/23 in silico tools predict a damaging outcome for this variant. 2/3 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_000089.4 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COL1A2 | NM_000089.4 | c.3106G>C | p.Gly1036Arg | missense_variant, splice_region_variant | 47/52 | ENST00000297268.11 | NP_000080.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COL1A2 | ENST00000297268.11 | c.3106G>C | p.Gly1036Arg | missense_variant, splice_region_variant | 47/52 | 1 | NM_000089.4 | ENSP00000297268.6 | ||
COL1A2 | ENST00000481570.5 | n.3556G>C | non_coding_transcript_exon_variant | 5/8 | 2 | |||||
COL1A2 | ENST00000488121.1 | n.22G>C | splice_region_variant, non_coding_transcript_exon_variant | 2/3 | 2 | |||||
COL1A2 | ENST00000492110.1 | n.226G>C | non_coding_transcript_exon_variant | 1/2 | 2 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 33
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Short fetal femur length Pathogenic:1
Pathogenic, no assertion criteria provided | research | Department of Genetics, Beijing BioBiggen Technology Co., Ltd. | Jun 29, 2022 | - - |
See cases Pathogenic:1
Pathogenic, no assertion criteria provided | research | Institute Of Reproduction And Development, Obstetrics and Gynecology Hospital, Fudan University | Jul 21, 2021 | - - |
Osteogenesis imperfecta with normal sclerae, dominant form Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Department of Medical Sciences, Uppsala University | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at