rs1429038624
Positions:
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP3BS1_Supporting
The ENST00000253008.3(PRDM12):c.1044_1045insACC(p.Ala348_Ala349insThr) variant causes a inframe insertion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 662,116 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★★).
Frequency
Genomes: 𝑓 0.000056 ( 0 hom., cov: 30)
Exomes 𝑓: 0.000017 ( 0 hom. )
Consequence
PRDM12
ENST00000253008.3 inframe_insertion
ENST00000253008.3 inframe_insertion
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.595
Genes affected
PRDM12 (HGNC:13997): (PR/SET domain 12) This gene encodes a transcriptional regulator of sensory neuronal specification that plays a critical role in pain perception. The encoded protein contains an N-terminal PRDI-BF1 and RIZ homology (PR) domain, a SET domain, and three C-terminal C2H2 zinc finger DNA-binding domains. Naturally occurring mutations in this gene are associated with congenital insensitivity to pain (CIP), and hereditary sensory and autonomic neuropathies (HSAN's) affecting peripheral sensory and autonomic neurons. Deregulation of this gene is associated with solid cancers and hematological malignancies including chronic myeloid leukaemia. [provided by RefSeq, Mar 2017]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 0 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP3
Nonframeshift variant in repetitive region in ENST00000253008.3
BS1
Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0000564 (7/124006) while in subpopulation EAS AF= 0.00237 (7/2952). AF 95% confidence interval is 0.00111. There are 0 homozygotes in gnomad4. There are 6 alleles in male gnomad4 subpopulation. Median coverage is 30. This position pass quality control queck. Existence of Clinvar submissions makes me limit the strength of this signal to Supporting
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PRDM12 | NM_021619.3 | c.1044_1045insACC | p.Ala348_Ala349insThr | inframe_insertion | 5/5 | ENST00000253008.3 | NP_067632.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRDM12 | ENST00000253008.3 | c.1044_1045insACC | p.Ala348_Ala349insThr | inframe_insertion | 5/5 | 1 | NM_021619.3 | ENSP00000253008 | P1 | |
PRDM12 | ENST00000676323.1 | c.906+138_906+139insACC | intron_variant | ENSP00000502471 |
Frequencies
GnomAD3 genomes AF: 0.0000565 AC: 7AN: 123948Hom.: 0 Cov.: 30
GnomAD3 genomes
AF:
AC:
7
AN:
123948
Hom.:
Cov.:
30
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
GnomAD4 exome AF: 0.0000167 AC: 9AN: 538110Hom.: 0 Cov.: 6 AF XY: 0.0000121 AC XY: 3AN XY: 248358
GnomAD4 exome
AF:
AC:
9
AN:
538110
Hom.:
Cov.:
6
AF XY:
AC XY:
3
AN XY:
248358
Gnomad4 AFR exome
AF:
Gnomad4 AMR exome
AF:
Gnomad4 ASJ exome
AF:
Gnomad4 EAS exome
AF:
Gnomad4 SAS exome
AF:
Gnomad4 FIN exome
AF:
Gnomad4 NFE exome
AF:
Gnomad4 OTH exome
AF:
GnomAD4 genome AF: 0.0000564 AC: 7AN: 124006Hom.: 0 Cov.: 30 AF XY: 0.0000996 AC XY: 6AN XY: 60212
GnomAD4 genome
AF:
AC:
7
AN:
124006
Hom.:
Cov.:
30
AF XY:
AC XY:
6
AN XY:
60212
Gnomad4 AFR
AF:
Gnomad4 AMR
AF:
Gnomad4 ASJ
AF:
Gnomad4 EAS
AF:
Gnomad4 SAS
AF:
Gnomad4 FIN
AF:
Gnomad4 NFE
AF:
Gnomad4 OTH
AF:
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
Congenital insensitivity to pain-hypohidrosis syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Aug 16, 2022 | This variant, c.1044_1045insACC, results in the insertion of 1 amino acid(s) of the PRDM12 protein (p.Ala348_Ala349insThr), but otherwise preserves the integrity of the reading frame. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with PRDM12-related conditions. ClinVar contains an entry for this variant (Variation ID: 475804). Experimental studies and prediction algorithms are not available or were not evaluated, and the functional significance of this variant is currently unknown. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 16, 2023 | The c.1044_1045insACC (p.A348_A349insT) alteration, located in coding exon 5 of the PRDM12 gene, results from an in-frame insertion of 3 nucleotides at positions c.1044 to c.1045. This results in the insertion of a threonine residue at p.348 to p.349. Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at