rs80358192

chr1-36098332-A-Cchr1-36098332-A-G

Variant summary

Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2 PP5

The NM_005202.4(COL8A2):c.1349T>G(p.Leu450Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000286 in 1,398,282 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency:
  • Genomes: not found (cov: 33)
  • Exomes 𝑓: 0.0000029 (0 hom.)
• Consequence: COL8A2 NM_005202.4 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:2
• Conservation: PhyloP100: 0.879

Genes affected

COL8A2 (HGNC:2216): (collagen type VIII alpha 2 chain) This gene encodes the alpha 2 chain of type VIII collagen. This protein is a major component of the basement membrane of the corneal endothelium and forms homo- or heterotrimers with alpha 1 (VIII) type collagens. Defects in this gene are associated with Fuchs endothelial corneal dystrophy and posterior polymorphous corneal dystrophy type 2. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014]

ACMG classification

Verdict is Uncertain_significance. Variant got 3 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-36098332-A-C is Pathogenic according to our data. Variant chr1-36098332-A-C is described in ClinVar as [Pathogenic]. Clinvar id is 17148.Status of the report is no_assertion_criteria_provided, 0 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
COL8A2	NM_005202.4	c.1349T>G	p.Leu450Trp	missense_variant	4/4	ENST00000397799.2
COL8A2	NM_001294347.2	c.1154T>G	p.Leu385Trp	missense_variant	4/4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
COL8A2	ENST00000397799.2	c.1349T>G	p.Leu450Trp	missense_variant	4/4	5	NM_005202.4	P2
COL8A2	ENST00000481785.1	c.1154T>G	p.Leu385Trp	missense_variant	2/2	1		A2
COL8A2	ENST00000303143.9	c.1349T>G	p.Leu450Trp	missense_variant	2/2	2		P2

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome AF: 0.00000286 AC: 4 AN: 1398282 Hom.: 0 Cov.: 37 AF XY: 0.00 AC XY: 0 AN XY: 689900

Gnomad4 AFR exome AF: 0.00

Gnomad4 AMR exome AF: 0.00

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00000370

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:2

Revision: no assertion criteria provided

Submissions by phenotype

Posterior polymorphous corneal dystrophy 2 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 28, 2013

- -

Corneal dystrophy, Fuchs endothelial, 1 Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Mar 28, 2013

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.17
BayesDel_addAF	Pathogenic	0.22	D
BayesDel_noAF	Uncertain	0.090
Cadd	Benign	23
Dann	Benign	0.92
DEOGEN2	Benign	0.30	T;T;.
Eigen	Benign	0.027
Eigen_PC	Benign	0.000047
FATHMM_MKL	Benign	0.12	N
M_CAP	Uncertain	0.20	D
MetaRNN	Uncertain	0.48	T;T;T
MetaSVM	Uncertain	0.085	D
MutationAssessor	Benign	2.0	M;M;.
MutationTaster	Benign	1.0	N;N;N
PrimateAI	Uncertain	0.49	T
PROVEAN	Benign	-1.1	N;N;N
REVEL	Uncertain	0.63
Sift	Uncertain	0.028	D;D;T
Sift4G	Uncertain	0.018	D;D;D
Polyphen		0.93	P;P;.
Vest4		0.34
MutPred		0.74		Loss of catalytic residue at L450 (P = 0.0892);Loss of catalytic residue at L450 (P = 0.0892);.;
MVP		0.95
MPC		0.50
ClinPred		0.20	T
GERP RS		4.4
Varity_R		0.090
gMVP		0.47

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

Other links and lift over

dbSNP: rs80358192; hg19: chr1-36563933;