NM_001508.3:c.1176G>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001508.3(GPR39):c.1176G>T(p.Leu392Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000558 in 1,613,374 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001508.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GPR39 | ENST00000329321.4 | c.1176G>T | p.Leu392Phe | missense_variant | Exon 2 of 2 | 1 | NM_001508.3 | ENSP00000327417.3 | ||
LYPD1 | ENST00000397463 | c.*625C>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_144586.7 | ENSP00000380605.2 | |||
GPR39 | ENST00000470071.1 | n.879G>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000403 AC: 1AN: 247934Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134346
GnomAD4 exome AF: 0.00000479 AC: 7AN: 1461174Hom.: 0 Cov.: 32 AF XY: 0.00000413 AC XY: 3AN XY: 726908
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152200Hom.: 0 Cov.: 33 AF XY: 0.0000135 AC XY: 1AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1176G>T (p.L392F) alteration is located in exon 2 (coding exon 2) of the GPR39 gene. This alteration results from a G to T substitution at nucleotide position 1176, causing the leucine (L) at amino acid position 392 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at