rs1040431132
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP3_Strong
The NM_016454.4(EMC4):āc.485C>Gā(p.Ser162Trp) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000205 in 1,461,616 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 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. S162L) has been classified as Uncertain significance.
Frequency
Consequence
NM_016454.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EMC4 | NM_016454.4 | c.485C>G | p.Ser162Trp | missense_variant | Exon 4 of 5 | ENST00000267750.9 | NP_057538.1 | |
EMC4 | NM_001351373.2 | c.242C>G | p.Ser81Trp | missense_variant | Exon 4 of 5 | NP_001338302.1 | ||
EMC4 | NM_001286420.2 | c.355+712C>G | intron_variant | Intron 3 of 3 | NP_001273349.1 | |||
EMC4 | NR_147140.2 | n.462+712C>G | intron_variant | Intron 3 of 3 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000205 AC: 3AN: 1461616Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727110
GnomAD4 genome Cov.: 32
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at