NM_000337.6:c.89G>T
Variant summary
Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B.
The NM_000337.6(SGCD):c.89G>T(p.Trp30Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,460,224 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. W30S) has been classified as Uncertain significance.
Frequency
Consequence
NM_000337.6 missense
Scores
Clinical Significance
Conservation
Publications
- autosomal recessive limb-girdle muscular dystrophyInheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
- autosomal recessive limb-girdle muscular dystrophy type 2FInheritance: AR Classification: DEFINITIVE, STRONG, MODERATE, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Orphanet, Myriad Women’s Health, Ambry Genetics
- familial isolated dilated cardiomyopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- dilated cardiomyopathyInheritance: AD Classification: LIMITED Submitted by: ClinGen
- dilated cardiomyopathy 1LInheritance: AD Classification: NO_KNOWN Submitted by: Ambry Genetics
Genome browser will be placed here
ACMG classification
Our verdict: Likely_pathogenic. The variant received 6 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SGCD | ENST00000337851.9 | c.89G>T | p.Trp30Leu | missense_variant | Exon 3 of 9 | 1 | NM_000337.6 | ENSP00000338343.4 | ||
SGCD | ENST00000435422.7 | c.86G>T | p.Trp29Leu | missense_variant | Exon 2 of 8 | 1 | ENSP00000403003.2 | |||
SGCD | ENST00000517913.5 | c.89G>T | p.Trp30Leu | missense_variant | Exon 5 of 10 | 5 | ENSP00000429378.1 | |||
SGCD | ENST00000524347.2 | n.89G>T | non_coding_transcript_exon_variant | Exon 3 of 6 | 5 | ENSP00000430794.1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.00000404 AC: 1AN: 247712 AF XY: 0.00000744 show subpopulations
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1460224Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 726352 show subpopulations ⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.
Age Distribution
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000657 AC: 1AN: 152236Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74432 show subpopulations
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at