chr3-48582512-C-T
Variant summary
Our verdict is Likely pathogenic. The variant received 6 ACMG points: 6P and 0B. PM1PM2PP3PP5
The NM_000094.4(COL7A1):c.4565G>A(p.Gly1522Glu) variant causes a missense, splice region change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. 14/24 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_000094.4 missense, splice_region
Scores
Clinical Significance
Conservation
Publications
- epidermolysis bullosa with congenital localized absence of skin and deformity of nailsInheritance: AD, AR Classification: DEFINITIVE, STRONG Submitted by: PanelApp Australia, G2P, Labcorp Genetics (formerly Invitae), Genomics England PanelApp
- dystrophic epidermolysis bullosa pruriginosaInheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, G2P, Orphanet
- recessive dystrophic epidermolysis bullosaInheritance: AR, AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: PanelApp Australia, Orphanet, Genomics England PanelApp, Ambry Genetics, G2P, ClinGen
- generalized dominant dystrophic epidermolysis bullosaInheritance: AD Classification: STRONG, SUPPORTIVE Submitted by: Genomics England PanelApp, Labcorp Genetics (formerly Invitae), PanelApp Australia, Orphanet
- pretibial dystrophic epidermolysis bullosaInheritance: AD, AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
- transient bullous dermolysis of the newbornInheritance: AD, AR Classification: STRONG, SUPPORTIVE Submitted by: Orphanet, Genomics England PanelApp
- acral dystrophic epidermolysis bullosaInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- dystrophic epidermolysis bullosa, nails onlyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- recessive dystrophic epidermolysis bullosa inversaInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- recessive dystrophic epidermolysis bullosa-generalized otherInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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 |
---|---|---|---|---|---|---|---|---|---|---|
COL7A1 | ENST00000681320.1 | c.4565G>A | p.Gly1522Glu | missense_variant, splice_region_variant | Exon 46 of 119 | NM_000094.4 | ENSP00000506558.1 | |||
COL7A1 | ENST00000328333.12 | c.4565G>A | p.Gly1522Glu | missense_variant, splice_region_variant | Exon 45 of 118 | 1 | ENSP00000332371.8 | |||
COL7A1 | ENST00000487017.5 | n.482G>A | splice_region_variant, non_coding_transcript_exon_variant | Exon 11 of 83 | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 34
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Transient bullous dermolysis of the newborn Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at