rs1057515420
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PM2PP3_StrongPP5
The NM_004444.5(EPHB4):c.980C>T(p.Pro327Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000144 in 1,393,024 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (no stars). Synonymous variant affecting the same amino acid position (i.e. P327P) has been classified as Likely benign.
Frequency
Consequence
NM_004444.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EPHB4 | NM_004444.5 | c.980C>T | p.Pro327Leu | missense_variant | 6/17 | ENST00000358173.8 | |
EPHB4 | XM_017011816.2 | c.980C>T | p.Pro327Leu | missense_variant | 6/17 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EPHB4 | ENST00000358173.8 | c.980C>T | p.Pro327Leu | missense_variant | 6/17 | 1 | NM_004444.5 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 0.00000144 AC: 2AN: 1393024Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 685910
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Tetralogy of Fallot Pathogenic:1
Likely pathogenic, no assertion criteria provided | research | Andelfinger Lab, Centre de Recherche, CHU Sainte Justine | Jan 01, 2015 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at