chr1-209633079-T-G

Position:

• chr1-209633079-T-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2 PP5 BP4

The NM_000228.3(LAMB3):​c.619A>C​(p.Lys207Gln) 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. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).

• Frequency: Genomes: not found (cov: 33)
• Consequence: LAMB3 NM_000228.3 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.11

Genes affected

LAMB3 (HGNC:6490): (laminin subunit beta 3) The product encoded by this gene is a laminin that belongs to a family of basement membrane proteins. This protein is a beta subunit laminin, which together with an alpha and a gamma subunit, forms laminin-5. Mutations in this gene cause epidermolysis bullosa junctional Herlitz type, and generalized atrophic benign epidermolysis bullosa, diseases that are characterized by blistering of the skin. Multiple alternatively spliced transcript variants that encode the same protein have been found for this gene. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• PP5: Variant 1-209633079-T-G is Pathogenic according to our data. Variant chr1-209633079-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 14552.Status of the report is no_assertion_criteria_provided, 0 stars.
• BP4: Computational evidence support a benign effect (MetaRNN=0.33696747). . Strength limited to SUPPORTING due to the PP5.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LAMB3	NM_000228.3	c.619A>C	p.Lys207Gln	missense_variant	7/23	ENST00000356082.9	NP_000219.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LAMB3	ENST00000356082.9	c.619A>C	p.Lys207Gln	missense_variant	7/23	1	NM_000228.3	ENSP00000348384	P1
LAMB3	ENST00000367030.7	c.619A>C	p.Lys207Gln	missense_variant	7/23	1		ENSP00000355997	P1
LAMB3	ENST00000391911.5	c.619A>C	p.Lys207Gln	missense_variant	6/22	1		ENSP00000375778	P1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Cov.: 30

GnomAD4 genome Cov.: 33

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:1

Revision: no assertion criteria provided

Submissions by phenotype

Junctional epidermolysis bullosa, non-Herlitz type Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

May 01, 2007

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.070	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	23
DANN	Uncertain	0.99
DEOGEN2	Benign	0.19	T;T;T
Eigen	Uncertain	0.25
Eigen_PC	Uncertain	0.25
FATHMM_MKL	Uncertain	0.82	D
LIST_S2	Benign	0.73	.;T;.
M_CAP	Benign	0.072	D
MetaRNN	Benign	0.34	T;T;T
MetaSVM	Benign	-0.56	T
MutationAssessor	Uncertain	2.0	M;M;M
MutationTaster	Benign	0.84	N;N;N
PrimateAI	Benign	0.48	T
PROVEAN	Benign	-0.55	N;N;N
REVEL	Uncertain	0.32
Sift	Benign	0.049	D;D;D
Sift4G	Benign	0.12	T;T;T
Polyphen		0.98	D;D;D
Vest4		0.35
MutPred		0.55		Loss of methylation at K207 (P = 0.0092);Loss of methylation at K207 (P = 0.0092);Loss of methylation at K207 (P = 0.0092);
MVP		0.86
MPC		0.39
ClinPred		0.83	D
GERP RS		4.7
Varity_R		0.24
gMVP		0.40

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: rs121912487; hg19: chr1-209806424;