rs267606657
Variant summary
Our verdict is Likely pathogenic. Variant got 8 ACMG points: 8P and 0B. PM2PP2PP3_StrongPP5
The NM_054027.6(ANKH):āc.1001T>Gā(p.Leu334Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,590 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 Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L334V) has been classified as Likely benign.
Frequency
Consequence
NM_054027.6 missense
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 |
---|---|---|---|---|---|---|---|
ANKH | NM_054027.6 | c.1001T>G | p.Leu334Arg | missense_variant | 8/12 | ENST00000284268.8 | |
ANKH | XM_017009644.3 | c.917T>G | p.Leu306Arg | missense_variant | 8/12 | ||
ANKH | XM_011514067.2 | c.1001T>G | p.Leu334Arg | missense_variant | 8/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ANKH | ENST00000284268.8 | c.1001T>G | p.Leu334Arg | missense_variant | 8/12 | 1 | NM_054027.6 | P1 | |
ANKH | ENST00000503939.5 | n.513T>G | non_coding_transcript_exon_variant | 5/6 | 3 | ||||
ANKH | ENST00000515517.1 | n.235T>G | non_coding_transcript_exon_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome AF: 6.84e-7 AC: 1AN: 1461590Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 727120
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Craniometaphyseal dysplasia, autosomal dominant Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2010 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at