chr9-133351913-TCACA-T
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PVS1_StrongPM2PP5_Moderate
The NM_003172.4(SURF1):c.899_902del(p.Val300AspfsTer44) variant causes a frameshift, stop lost change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Likely pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. V300V) has been classified as Likely benign.
Frequency
Consequence
NM_003172.4 frameshift, stop_lost
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_pathogenic. Variant got 8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SURF1 | NM_003172.4 | c.899_902del | p.Val300AspfsTer44 | frameshift_variant, stop_lost | 9/9 | ENST00000371974.8 | |
SURF1 | NM_001280787.1 | c.572_575del | p.Val191AspfsTer? | frameshift_variant, stop_lost | 8/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SURF1 | ENST00000371974.8 | c.899_902del | p.Val300AspfsTer44 | frameshift_variant, stop_lost | 9/9 | 1 | NM_003172.4 | P1 | |
SURF1 | ENST00000615505.4 | c.572_575del | p.Val191AspfsTer? | frameshift_variant, stop_lost | 8/8 | 1 | |||
SURF1 | ENST00000437995.1 | n.809_812del | non_coding_transcript_exon_variant | 8/8 | 5 | ||||
SURF1 | ENST00000495952.5 | n.889_892del | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
Mitochondrial complex IV deficiency, nuclear type 1 Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Laboratory of Inherited Metabolic Diseases, Research centre for medical genetics | Jan 31, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.