GeneBe

rs534023088

Variant names:

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The NM_007046.4(EMILIN1):​c.101G>A​(p.Gly34Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. G34V) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)

Consequence

EMILIN1
NM_007046.4 missense

Scores

4
14

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.23

Publications

0 publications found
Variant links:
Genes affected
EMILIN1 (HGNC:19880): (elastin microfibril interfacer 1) This gene encodes an extracellular matrix glycoprotein that is characterized by an N-terminal microfibril interface domain, a coiled-coiled alpha-helical domain, a collagenous domain and a C-terminal globular C1q domain. The encoded protein associates with elastic fibers at the interface between elastin and microfibrils and may play a role in the development of elastic tissues including large blood vessels, dermis, heart and lung. [provided by RefSeq, Sep 2009]
EMILIN1 Gene-Disease associations (from GenCC):
  • arterial tortuosity-bone fragility syndrome
    Inheritance: AR Classification: DEFINITIVE Submitted by: ClinGen
  • neuronopathy, distal hereditary motor, autosomal dominant 10
    Inheritance: AD Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)

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ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_007046.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EMILIN1
NM_007046.4
MANE Select
c.101G>Ap.Gly34Asp
missense
Exon 1 of 8NP_008977.1Q9Y6C2-1

Ensembl Transcripts

Sel.
GeneTranscriptTagsHGVScHGVSpEffectExon RankProteinUniProt
EMILIN1
ENST00000380320.9
TSL:1 MANE Select
c.101G>Ap.Gly34Asp
missense
Exon 1 of 8ENSP00000369677.4Q9Y6C2-1
EMILIN1
ENST00000957377.1
c.101G>Ap.Gly34Asp
missense
Exon 1 of 8ENSP00000627436.1
EMILIN1
ENST00000957375.1
c.101G>Ap.Gly34Asp
missense
Exon 1 of 7ENSP00000627434.1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD2 exomes
AF:
0.00
AC:
0
AN:
212476
AF XY:
0.00
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
31
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
0.40
BayesDel_addAF
Benign
-0.040
T
BayesDel_noAF
Benign
-0.30
CADD
Benign
17
DANN
Benign
0.94
DEOGEN2
Benign
0.13
T
Eigen
Benign
-0.59
Eigen_PC
Benign
-0.64
FATHMM_MKL
Benign
0.67
D
LIST_S2
Benign
0.74
T
M_CAP
Benign
0.054
D
MetaRNN
Uncertain
0.61
D
MetaSVM
Benign
-0.96
T
MutationAssessor
Benign
0.34
N
PhyloP100
2.2
PrimateAI
Uncertain
0.73
T
PROVEAN
Benign
-1.1
N
REVEL
Uncertain
0.34
Sift
Benign
0.054
T
Sift4G
Benign
0.15
T
Polyphen
0.70
P
Vest4
0.73
MutPred
0.14
Loss of catalytic residue at S36 (P = 0.0387)
MVP
0.76
MPC
0.73
ClinPred
0.31
T
GERP RS
1.7
Varity_R
0.076
gMVP
0.71
Mutation Taster
=90/10
polymorphism

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

Other links and lift over

dbSNP: rs534023088; hg19: chr2-27302034; API