3-48582346-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4

The NM_000094.4(COL7A1):​c.4612C>G​(p.Arg1538Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

COL7A1
NM_000094.4 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.382
Variant links:
Genes affected
COL7A1 (HGNC:2214): (collagen type VII alpha 1 chain) This gene encodes the alpha chain of type VII collagen. The type VII collagen fibril, composed of three identical alpha collagen chains, is restricted to the basement zone beneath stratified squamous epithelia. It functions as an anchoring fibril between the external epithelia and the underlying stroma. Mutations in this gene are associated with all forms of dystrophic epidermolysis bullosa. In the absence of mutations, however, an acquired form of this disease can result from an autoimmune response made to type VII collagen. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in the COL7A1 gene, where missense mutations are typically associated with disease (based on misZ statistic). The gene has 223 curated pathogenic missense variants (we use a threshold of 10). The gene has 262 curated benign missense variants. Gene score misZ: 1.5899 (below the threshold of 3.09). Trascript score misZ: 4.0428 (above the threshold of 3.09). GenCC associations: The gene is linked to recessive dystrophic epidermolysis bullosa, dystrophic epidermolysis bullosa pruriginosa, recessive dystrophic epidermolysis bullosa-generalized other, transient bullous dermolysis of the newborn, epidermolysis bullosa with congenital localized absence of skin and deformity of nails, generalized dominant dystrophic epidermolysis bullosa, dystrophic epidermolysis bullosa, nails only, acral dystrophic epidermolysis bullosa, recessive dystrophic epidermolysis bullosa inversa, pretibial dystrophic epidermolysis bullosa.
BP4
Computational evidence support a benign effect (MetaRNN=0.37212467).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
COL7A1NM_000094.4 linkc.4612C>G p.Arg1538Gly missense_variant Exon 47 of 119 ENST00000681320.1 NP_000085.1 Q02388-1Q59F16

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
COL7A1ENST00000681320.1 linkc.4612C>G p.Arg1538Gly missense_variant Exon 47 of 119 NM_000094.4 ENSP00000506558.1 Q02388-1
COL7A1ENST00000328333.12 linkc.4612C>G p.Arg1538Gly missense_variant Exon 46 of 118 1 ENSP00000332371.8 Q02388-1
COL7A1ENST00000487017.5 linkn.529C>G non_coding_transcript_exon_variant Exon 12 of 83 5

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
34
GnomAD4 genome
Cov.:
32
Bravo
AF:
0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.12
BayesDel_addAF
Uncertain
0.074
D
BayesDel_noAF
Benign
-0.13
CADD
Uncertain
23
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.53
D
Eigen
Uncertain
0.24
Eigen_PC
Benign
0.21
FATHMM_MKL
Benign
0.14
N
LIST_S2
Benign
0.74
T
M_CAP
Benign
0.035
D
MetaRNN
Benign
0.37
T
MetaSVM
Uncertain
0.12
D
MutationAssessor
Benign
0.45
N
PrimateAI
Benign
0.45
T
PROVEAN
Benign
-1.3
N
REVEL
Uncertain
0.37
Sift
Benign
0.30
T
Sift4G
Benign
0.45
T
Polyphen
0.98
D
Vest4
0.37
MutPred
0.50
Loss of glycosylation at K1533 (P = 0.0046);
MVP
0.89
MPC
0.32
ClinPred
0.41
T
GERP RS
4.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.24
gMVP
0.92

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs149711883; hg19: chr3-48619779; API