rs1457098622
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PM5PP3_Strong
The NM_000070.3(CAPN3):āc.2330T>Cā(p.Ile777Thr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,872 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 Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I777V) has been classified as Pathogenic.
Frequency
Consequence
NM_000070.3 missense
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 |
---|---|---|---|---|---|---|---|---|
CAPN3 | NM_000070.3 | c.2330T>C | p.Ile777Thr | missense_variant | 22/24 | ENST00000397163.8 | NP_000061.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAPN3 | ENST00000397163.8 | c.2330T>C | p.Ile777Thr | missense_variant | 22/24 | 1 | NM_000070.3 | ENSP00000380349.3 | ||
CAPN3 | ENST00000673886.1 | c.335T>C | p.Ile112Thr | missense_variant | 9/11 | ENSP00000501155.1 | ||||
CAPN3 | ENST00000673928.1 | c.335T>C | p.Ile112Thr | missense_variant | 9/11 | ENSP00000501099.1 | ||||
CAPN3 | ENST00000674146.1 | c.335T>C | p.Ile112Thr | missense_variant | 10/12 | ENSP00000501175.1 | ||||
CAPN3 | ENST00000674149.1 | c.335T>C | p.Ile112Thr | missense_variant | 9/11 | ENSP00000501112.1 | ||||
CAPN3 | ENST00000673743.1 | c.233T>C | p.Ile78Thr | missense_variant | 9/11 | ENSP00000500989.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*2766T>C | non_coding_transcript_exon_variant | 24/26 | 2 | ENSP00000492063.1 | ||||
ENSG00000258461 | ENST00000495723.1 | n.*2766T>C | 3_prime_UTR_variant | 24/26 | 2 | ENSP00000492063.1 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251414Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135870
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461872Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727238
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Autosomal recessive limb-girdle muscular dystrophy type 2A Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Aug 02, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at