chrX-23334990-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_173495.3(PTCHD1):c.115C>T(p.Leu39Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000048 in 1,208,424 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 24 hemizygotes in GnomAD. Variant has been reported in ClinVar as Uncertain significance (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L39H) has been classified as Uncertain significance.
Frequency
Consequence
NM_173495.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PTCHD1 | NM_173495.3 | c.115C>T | p.Leu39Phe | missense_variant | 1/3 | ENST00000379361.5 | |
PTCHD1 | XM_011545449.4 | c.115C>T | p.Leu39Phe | missense_variant | 2/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PTCHD1 | ENST00000379361.5 | c.115C>T | p.Leu39Phe | missense_variant | 1/3 | 1 | NM_173495.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000899 AC: 1AN: 111278Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33494
GnomAD3 exomes AF: 0.0000168 AC: 3AN: 178182Hom.: 0 AF XY: 0.0000154 AC XY: 1AN XY: 65018
GnomAD4 exome AF: 0.0000520 AC: 57AN: 1097146Hom.: 0 Cov.: 31 AF XY: 0.0000634 AC XY: 23AN XY: 362642
GnomAD4 genome ? AF: 0.00000899 AC: 1AN: 111278Hom.: 0 Cov.: 23 AF XY: 0.0000299 AC XY: 1AN XY: 33494
ClinVar
Submissions by phenotype
Autism, susceptibility to, X-linked 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Feb 24, 2022 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2016 | The p.L39F variant (also known as c.115C>T), located in coding exon 1 of the PTCHD1 gene, results from a C to T substitution at nucleotide position 115. The leucine at codon 39 is replaced by phenylalanine, an amino acid with highly similar properties. This variant was not reported in population based cohorts in the following databases: Database of Single Nucleotide Polymorphisms (dbSNP), NHLBI Exome Sequencing Project (ESP), and 1000 Genomes Project. In the ESP, this variant was not observed in 6413 samples with coverage at this position. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at