chr2-132645415-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001508.3(GPR39):c.1171C>T(p.Pro391Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. 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. P391R) has been classified 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.1171C>T | p.Pro391Ser | missense_variant | Exon 2 of 2 | 1 | NM_001508.3 | ENSP00000327417.3 | ||
LYPD1 | ENST00000397463 | c.*630G>A | 3_prime_UTR_variant | Exon 3 of 3 | 1 | NM_144586.7 | ENSP00000380605.2 | |||
GPR39 | ENST00000470071.1 | n.874C>T | non_coding_transcript_exon_variant | Exon 3 of 3 | 2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1171C>T (p.P391S) alteration is located in exon 2 (coding exon 2) of the GPR39 gene. This alteration results from a C to T substitution at nucleotide position 1171, causing the proline (P) at amino acid position 391 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.