rs121434272
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP5
The NM_001126128.2(PROK2):c.217C>T(p.Arg73Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000514 in 1,613,836 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001126128.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PROK2 | ENST00000295619.4 | c.217C>T | p.Arg73Cys | missense_variant | Exon 2 of 4 | 1 | NM_001126128.2 | ENSP00000295619.3 | ||
PROK2 | ENST00000353065.7 | c.217C>T | p.Arg73Cys | missense_variant | Exon 2 of 3 | 1 | ENSP00000295618.3 |
Frequencies
GnomAD3 genomes AF: 0.0000592 AC: 9AN: 152074Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000716 AC: 18AN: 251420Hom.: 0 AF XY: 0.0000883 AC XY: 12AN XY: 135900
GnomAD4 exome AF: 0.0000506 AC: 74AN: 1461762Hom.: 0 Cov.: 30 AF XY: 0.0000674 AC XY: 49AN XY: 727192
GnomAD4 genome AF: 0.0000592 AC: 9AN: 152074Hom.: 0 Cov.: 32 AF XY: 0.0000808 AC XY: 6AN XY: 74286
ClinVar
Submissions by phenotype
Hypogonadotropic hypogonadism 4 with or without anosmia Pathogenic:3
- -
- -
- -
not provided Pathogenic:1Uncertain:1
ClinVar contains an entry for this variant (Variation ID: 3604). This sequence change replaces arginine with cysteine at codon 73 of the PROK2 protein (p.Arg73Cys). The arginine residue is highly conserved and there is a large physicochemical difference between arginine and cysteine. This variant is present in population databases (rs121434272, ExAC 0.02%). This missense change has been observed in individuals with clinical features of Kallman syndrome (PMID: 17054399, 18285834, 18559922, 26141714). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. Experimental studies have shown that this missense change affects PROK2 function (PMID: 18559922). 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. -
Reported as a single heterozygous variant in patients with primary amehorrhea or Kallman syndrome; however, this variant has also been reported in unaffected relatives (PMID: 17054399, 37988663, 29298845; Ozbek et al., 2014); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Published functional studies demonstrate that this variant decreases the activity of the PROK2 protein (PMID: 18559922); This variant is associated with the following publications: (PMID: 18285834, 30024674, 17054399, 26141714, 34426522, 31589614, 19707180, 37684054, 37988663, 36700485, 23596439, 29298845, 18559922) -
PROK2-related disorder Pathogenic:1
The PROK2 c.217C>T variant is predicted to result in the amino acid substitution p.Arg73Cys. This variant has been reported in the heterozygous, homozygous, or compound heterozygous state in patients affected with Kallmann syndrome and normosmic hypogonadotropic hypogonadism (Dodé et al. 2006. PubMed ID: 17054399; Cole et al. 2008. PubMed ID: 18559922; Leroy et al. 2008. PubMed ID: 18285834; Mao et al. 2015. PubMed ID: 26141714). This variant is expected to disrupt the formation of the disulfide bonds of the protein; in vitro functional analysis demonstrated that this variant resulted in a 7-fold decrease in calcium mobilization activity in the presence of PROK2 receptor (PROKR2) (Cole et al. 2008. PubMed ID: 18559922). This variant is reported in 0.039% of alleles in individuals of South Asian descent in gnomAD. This variant is interpreted as likely pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at