rs199476197
Variant summary
Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PM2PP3_StrongPP5_Very_Strong
The NM_207352.4(CYP4V2):c.992A>C(p.His331Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000013 in 1,614,076 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 Pathogenic (★★). Synonymous variant affecting the same amino acid position (i.e. H331H) has been classified as Likely benign.
Frequency
Consequence
NM_207352.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CYP4V2 | NM_207352.4 | c.992A>C | p.His331Pro | missense_variant | 8/11 | ENST00000378802.5 | |
CYP4V2 | XM_005262935.5 | c.992A>C | p.His331Pro | missense_variant | 8/11 | ||
CYP4V2 | XM_047450077.1 | c.596A>C | p.His199Pro | missense_variant | 6/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CYP4V2 | ENST00000378802.5 | c.992A>C | p.His331Pro | missense_variant | 8/11 | 1 | NM_207352.4 | P1 | |
CYP4V2 | ENST00000502665.1 | n.227A>C | non_coding_transcript_exon_variant | 2/5 | 1 | ||||
CYP4V2 | ENST00000507209.5 | n.5690A>C | non_coding_transcript_exon_variant | 3/6 | 1 | ||||
CYP4V2 | ENST00000513354.5 | n.82A>C | non_coding_transcript_exon_variant | 2/5 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000755 AC: 19AN: 251496Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135922
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461844Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727234
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74370
ClinVar
Submissions by phenotype
Bietti crystalline corneoretinal dystrophy Pathogenic:3
Pathogenic, no assertion criteria provided | literature only | OMIM | Jun 01, 2005 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | Aug 01, 2017 | The p.His331Pro (NM207352.3 c.992A>C) variant in CYP4V2 has been reported in at least 6 homozygous and 14 compound heterozygous individuals with Bietti crystall ine dystrophy and one family with retinitis pigmentosa (Huang 2015, Liu 2015, Yi n 2016, and Jiao 2017). In vitro functional studies on the p.His331Pro variant provide evidence supporting an impact on protein function (Nakano 2012). This va riant has been identified in 0.11% (19/17248) of East Asian chromosomes by the G enome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs19 9476197). Although this variant has been seen in the general population, its fre quency is low enough to be consistent with a recessive carrier frequency. In sum mary, this variant meets criteria to be classified as pathogenic for Bietti crys talline dystrophy in an autosomal recessive manner based upon its biallelic occu rrence in affected individuals and impact in functional studies. - |
Pathogenic, no assertion criteria provided | curation | GeneReviews | Apr 12, 2012 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Jan 11, 2024 | This sequence change replaces histidine, which is basic and polar, with proline, which is neutral and non-polar, at codon 331 of the CYP4V2 protein (p.His331Pro). This variant is present in population databases (rs199476197, gnomAD 0.1%). This missense change has been observed in individual(s) with Bietti crystalline corneoretinal dystrophy (PMID: 15042513, 25611614, 26971461, 28848678). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 39275). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on CYP4V2 protein function. Experimental studies have shown that this missense change affects CYP4V2 function (PMID: 22772592). For these reasons, this variant has been classified as Pathogenic. - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Dec 24, 2018 | The H331P variant in the CYP4V2 gene has been reported previously in association with Bietti crystalline corneoretinal dystrophy (BCD), and is seen in 7.4% of alleles in the Chinese population with BCD (Xiao et al., 2011; Huang et al., 2015; Yin et al., 2016). The H331P variant is observed in 19/17248 (0.11%) alleles from individuals of East Asian background, in large population cohorts (Lek et al., 2016). The H331P variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Functional studies show H331P has significantly lower steady-state protein expression levels compared to wild type and lipid profiling data are consistent with reduced metabolism of polyunsaturated fatty acids for the H331P variant (Nakano et al., 2012). We interpret H331P as a pathogenic variant. - |
Retinal dystrophy Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Blueprint Genetics | May 05, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at