rs1057519325
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PM5PP3_ModeratePP5
The NM_001354604.2(MITF):c.939G>C(p.Lys313Asn) 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 pathogenic outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K313Q) has been classified as Uncertain significance.
Frequency
Consequence
NM_001354604.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MITF | NM_001354604.2 | c.939G>C | p.Lys313Asn | missense_variant | 7/10 | ENST00000352241.9 | |
MITF | NM_000248.4 | c.618G>C | p.Lys206Asn | missense_variant | 6/9 | ENST00000394351.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MITF | ENST00000352241.9 | c.939G>C | p.Lys313Asn | missense_variant | 7/10 | 1 | NM_001354604.2 | P4 | |
MITF | ENST00000394351.9 | c.618G>C | p.Lys206Asn | missense_variant | 6/9 | 1 | NM_000248.4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 30
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Coloboma, osteopetrosis, microphthalmia, macrocephaly, albinism, and deafness Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 15, 2017 | - - |
Waardenburg syndrome type 2A Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Aug 15, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at