10-13233314-TGGGGCCTCCTAACCCTGACAAAGTATTCAATCCAATATACGACCTACAGTCAGGAAATAGGGTGTAATTTCTCATTCAGAGCTGCAGTCCCTTTGATACCCTGGGGTGAGCCCTTCGTGCCCAGCTGCATCCTGCTGCCCGGCTGACTGTGGGAGAGGAGGAGCCGGGGGGTGTGAGCAGAGGTGGTGATGGACGCGGGATGGGGTCCCTCCAGCATCCTTACCATTGACCTCATCTCTGGACTTGGGGGACCGCTTGCCGCGCCTCTTGAGGAAATTCGAGGCATCTGATTCCTGCATGAAAATCTTCTGTTTTGCATCTGAAACCCGGGAGAGGCCTGTCACCAGCAGTGTGGGGGTGCTGGGGCTGCTGCTTCGCTGGCTGCACCTGCCCTGCCCCGTGGGTGGCCCCTGCACTCACCTTCACTCGCCTCTTCTCCCGCCATCTGCATGGTGCCCACAGATACACTGGTTCCCTCTCTCAGCACTGCAGGACAAGGGCACAGAGTGAGGCTGCAGCATCAGAGGGGAGCCCAGACCCTGAGCTGAGTCCCCATCTCTCTTTCCAGGCTAAGCGTCCTGCCAGGGCCTGGCAGGGGGCCCGTGGTTTCTCACGTACCAGCTGCAGAGCCAATCTCCCCAGGAACCCACCAAGCAAGCTGGCTTGGGTTTTTTTTCTATTTTGTTTCTTTCTTTACTGTTTTTTATTATTATTATTATTTTTCTGTATTGCATTGTGTCCTACATGCACACGACACACACATACACACATGTTAACAATAAGCATACTCCTTTCTACCTGCATCACCTGAGCAGCCTTACCTGTGCATGGTAAGTCTCCCTTACCATGTAACTAACACCCTCCACCTTGACCCTCCTGTACTCACTAGACAGGAGCACCACGGCGGAGAAGCAAGACAGCAGGACGG-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PM4
The NM_145314.3(UCMA):c.17_220+223del(p.Ala6_Asn73del) variant causes a conservative inframe deletion change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Consequence
UCMA
NM_145314.3 conservative_inframe_deletion
NM_145314.3 conservative_inframe_deletion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.915
Genes affected
UCMA (HGNC:25205): (upper zone of growth plate and cartilage matrix associated) This gene encodes a chondrocyte-specific, highly charged protein that is abundantly expressed in the upper immature zone of fetal and juvenile epiphyseal cartilage. The encoded protein undergoes proteolytic processing to generate a mature protein that is secreted into the extracellular matrix. The glutamic acid residues in the encoded protein undergo gamma carboxylation in a vitamin K-dependent manner. Undercarboxylation of the encoded protein is associated with osteoarthritis in humans. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2015]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 4 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PM4
Nonframeshift variant in NON repetitive region in NM_145314.3.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|
| UCMA | NM_145314.3 | c.17_220+223del | p.Ala6_Asn73del | conservative_inframe_deletion | 3/5 | ENST00000378681.8 | NP_660357.2 | |
| UCMA | NM_145314.3 | c.17_220+223del | exon_loss_variant | 3/5 | ENST00000378681.8 | NP_660357.2 | ||
| UCMA | NM_145314.3 | c.17_220+223del | exon_loss_variant | 2/5 | ENST00000378681.8 | NP_660357.2 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|---|
| UCMA | ENST00000378681.8 | c.17_220+223del | p.Ala6_Asn73del | conservative_inframe_deletion | 3/5 | 1 | NM_145314.3 | ENSP00000367952.3 | ||
| UCMA | ENST00000378681.8 | c.17_220+223del | exon_loss_variant | 3/5 | 1 | NM_145314.3 | ENSP00000367952.3 | |||
| UCMA | ENST00000378681.8 | c.17_220+223del | exon_loss_variant | 2/5 | 1 | NM_145314.3 | ENSP00000367952.3 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
GnomAD4 genome
Cov.:
32
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Uncertain:1
| Uncertain significance, criteria provided, single submitter | clinical testing | New York Genome Center | Apr 30, 2021 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.