NM_001370959.1:c.1310C>T
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 1P and 4B. PP3BS2
The NM_001370959.1(POU6F2):c.1310C>T(p.Pro437Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,613,816 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 Uncertain significance (★★).
Frequency
Consequence
NM_001370959.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
POU6F2 | NM_001370959.1 | c.1310C>T | p.Pro437Leu | missense_variant | Exon 7 of 10 | ENST00000518318.7 | NP_001357888.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POU6F2 | ENST00000518318.7 | c.1310C>T | p.Pro437Leu | missense_variant | Exon 7 of 10 | 1 | NM_001370959.1 | ENSP00000430514.3 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000120 AC: 3AN: 250620Hom.: 0 AF XY: 0.00000738 AC XY: 1AN XY: 135436
GnomAD4 exome AF: 0.0000315 AC: 46AN: 1461674Hom.: 0 Cov.: 32 AF XY: 0.0000344 AC XY: 25AN XY: 727114
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152142Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1223C>T (p.P408L) alteration is located in exon 8 (coding exon 7) of the POU6F2 gene. This alteration results from a C to T substitution at nucleotide position 1223, causing the proline (P) at amino acid position 408 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Hypogonadotropic hypogonadism Uncertain:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at