2-55867075-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 4P and 1B. PM2PP5_ModerateBP4
The NM_001039348.3(EFEMP1):c.1480T>C(p.Ter494GlnextTer29) variant causes a stop lost change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Pathogenic (★).
Frequency
Genomes: not found (cov: 32)
Consequence
EFEMP1
NM_001039348.3 stop_lost
NM_001039348.3 stop_lost
Scores
3
4
Clinical Significance
Conservation
PhyloP100: 8.61
Genes affected
EFEMP1 (HGNC:3218): (EGF containing fibulin extracellular matrix protein 1) This gene encodes a member of the fibulin family of extracellular matrix glycoproteins. Like all members of this family, the encoded protein contains tandemly repeated epidermal growth factor-like repeats followed by a C-terminus fibulin-type domain. This gene is upregulated in malignant gliomas and may play a role in the aggressive nature of these tumors. Mutations in this gene are associated with Doyne honeycomb retinal dystrophy. Alternatively spliced transcript variants that encode the same protein have been described.[provided by RefSeq, Nov 2009]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant 2-55867075-A-G is Pathogenic according to our data. Variant chr2-55867075-A-G is described in ClinVar as [Pathogenic]. Clinvar id is 1294422.Status of the report is criteria_provided_single_submitter, 1 stars.
BP4
?
Computational evidence support a benign effect (BayesDel_addAF=-0.0337291).. Strength limited to SUPPORTING due to the PP5.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EFEMP1 | NM_001039348.3 | c.1480T>C | p.Ter494GlnextTer29 | stop_lost | 12/12 | ENST00000355426.8 | |
LOC112268416 | XR_002959388.2 | n.229-6808A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EFEMP1 | ENST00000355426.8 | c.1480T>C | p.Ter494GlnextTer29 | stop_lost | 12/12 | 1 | NM_001039348.3 | P1 | |
EFEMP1 | ENST00000394555.6 | c.1480T>C | p.Ter494GlnextTer29 | stop_lost | 11/11 | 1 | P1 | ||
EFEMP1 | ENST00000634374.1 | c.841T>C | p.Ter281GlnextTer29 | stop_lost | 6/6 | 5 | |||
EFEMP1 | ENST00000635671.1 | c.*1132T>C | 3_prime_UTR_variant, NMD_transcript_variant | 9/9 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD3 genomes
?
Cov.:
32
GnomAD4 exome Cov.: 30
GnomAD4 exome
Cov.:
30
GnomAD4 genome ? Cov.: 32
GnomAD4 genome
?
Cov.:
32
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:3
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Glaucoma 1, open angle, H Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Mar 18, 2024 | - - |
not provided Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jun 21, 2023 | This sequence change disrupts the translational stop signal of the EFEMP1 mRNA. It is expected to extend the length of the EFEMP1 protein by 29 additional amino acid residues. For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this protein extension affects EFEMP1 function (PMID: 34923728). Algorithms developed to predict the effect of variants on protein structure and function are not available or were not evaluated for this variant. ClinVar contains an entry for this variant (Variation ID: 1294422). This protein extension has been observed in individual(s) with juvenile‚Äê onset primary open‚Äêangle glaucoma (PMID: 34923728). It has also been observed to segregate with disease in related individuals. This variant is not present in population databases (gnomAD no frequency). - |
Glaucoma of childhood Pathogenic:1
Pathogenic, no assertion criteria provided | research | Janey Wiggs Laboratory, Massachusetts Eye and Ear, Harvard Medical School | Sep 23, 2021 | The c.1480T>C variant in EFEMP1 causes the stop codon to be lost and adds an additional 29 amino acids to the C-terminus of the protein. This variant has been reported in a Filipino family (Collantes et al, in revision) and segregated with disease in 24 individuals (17 affected) and was absent from last population studies. Additionally, invitro functional studies indicate that c.1480T>C causes intracellular protein aggregation potentially related to disease pathogenesis. In summary the c.1480T>C variant meets criteria to be classified as pathogenic based upon segregation studies, absence from controls and functional evidence. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
MutationTaster
Benign
N;N;N;N
Vest4
GERP RS
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.