chr3-87262098-A-G
Variant summary
Our verdict is Likely pathogenic. Variant got 9 ACMG points: 9P and 0B. PM1PM2PP3_StrongPP5
The NM_000306.4(POU1F1):āc.577T>Cā(p.Trp193Arg) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000137 in 1,461,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. 12/21 in silico tools predict a damaging outcome for this variant. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Consequence
NM_000306.4 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 |
---|---|---|---|---|---|---|---|
POU1F1 | NM_000306.4 | c.577T>C | p.Trp193Arg | missense_variant | 4/6 | ENST00000350375.7 | |
POU1F1 | NM_001122757.3 | c.655T>C | p.Trp219Arg | missense_variant | 4/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
POU1F1 | ENST00000350375.7 | c.577T>C | p.Trp193Arg | missense_variant | 4/6 | 1 | NM_000306.4 | P4 | |
POU1F1 | ENST00000344265.8 | c.655T>C | p.Trp219Arg | missense_variant | 4/6 | 5 | A1 | ||
POU1F1 | ENST00000561167.5 | c.352T>C | p.Trp118Arg | missense_variant | 3/5 | 5 | |||
POU1F1 | ENST00000560656.1 | c.440-1994T>C | intron_variant | 5 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251146Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135712
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461816Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727208
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Pituitary hormone deficiency, combined, 1 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Apr 01, 2001 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at