NM_004425.4:c.826C>T
Variant summary
Our verdict is Pathogenic. The variant received 10 ACMG points: 10P and 0B. PVS1PM2
The NM_004425.4(ECM1):c.826C>T(p.Gln276*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,874 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 not provided (no stars). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_004425.4 stop_gained
Scores
Clinical Significance
Conservation
Publications
- lipoid proteinosisInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), Laboratory for Molecular Medicine, G2P, Orphanet
Genome browser will be placed here
ACMG classification
Our verdict: Pathogenic. The variant received 10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ECM1 | NM_004425.4 | c.826C>T | p.Gln276* | stop_gained | Exon 7 of 10 | ENST00000369047.9 | NP_004416.2 | |
ECM1 | NM_001202858.2 | c.907C>T | p.Gln303* | stop_gained | Exon 7 of 10 | NP_001189787.1 | ||
ECM1 | NM_022664.3 | c.708+376C>T | intron_variant | Intron 6 of 8 | NP_073155.2 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD2 exomes AF: 0.00000398 AC: 1AN: 251312 AF XY: 0.00 show subpopulations
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461874Hom.: 0 Cov.: 34 AF XY: 0.00000138 AC XY: 1AN XY: 727238 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Lipid proteinosis Other:1
South African founder variant [Hamada 2002, Van Hougenhouck-Tulleken et al 2004] -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at