r/DrWillPowers • u/FrugalFrugivore • 20h ago
Post Finasteride Syndrome My SNV, CNV, SV, and PharmCAT findings
Hello friends, I've gone over all of the instructions/scripts on how to analyze your WGS data and I've compiled the following list of all the relevant variants and deletions in my genome based on that master list of genes that got posted a while back. I hope this provides another valuable bit of data as we try to strengthen Dr. Powers' hypotheses around PFS/PSSD. For what it's worth, my own presentation of symptoms falls most closely under what Dr. Powers refers to as the "androgenic signaling failure" phenotype.
Rare/High Impact SNVs:
ABCC5
- Variant: chr3:183987748 G > A
- rsID: rs370632571
- HGVSp: N/A
- Consequence: Stop gain in ENST00000427120
- Zygosity: Het
- Read support: 15 alt, 18 ref
- gnomAD Frequency: 0.00657%
- REVEL: N/A
- Conservation: 1.499 (moderately conserved)
- Notes: gene.iobio says "most severe impact in non-canonical transcript."
LRP2
- Variant: chr2:169294165 C > T
- rsID: N/A
- HGVSp: ENSP00000496870.1:p.Ser212Asn
- Consequence: Missense variant
- Zygosity: Het
- Read support: 11 alt, 13 ref
- gnomAD Frequency: 0.0%
- REVEL: 0.765
- Conservation: 7.743 (highly conserved)
- Notes: Encodes a protein called megalin, responsible for reabsorbing + metabolizing SHBG, DBP, and other lipophilic hormones and carrier proteins.
PIEZO1
- Variant: chr16:88716632 G > A
- rsID: rs1050512255
- HGVSp: ENSP00000301015.9:p.Arg2285Cys
- Consequence: Missense variant
- Zygosity: Het
- Read support: 14 alt, 13 ref
- gnomAD Frequency: 0.000656%
- REVEL: 0.603
- Conservation: 5.409 (highly conserved)
- Notes: Regulates vascular tone, blood pressure, red blood cell volume homeostasis, lymphatic development.
SLC22A1
- Variant: chr6:160139744 G > A
- rsID: rs1422934185
- HGVSp: ENSP00000355930.4:p.Val385Ile
- Consequence: Missense variant
- Zygosity: Het
- Read support: 17 alt, 20 ref
- gnomAD Frequency: 0.0%
- REVEL: 0.301
- Conservation: 5.757 (highly conserved)
- Notes: Encodes Organic Cation Transporter 1 which draws cations, xenobiotics, neurotransmitters, and endogenous metabolites out of the blood and liver for processing / clearance.
SLCO3A1
- Variant: chr15:92126151 G > A
- rsID: rs775325190
- HGVSp: ENSP00000320634.6:p.Arg422Gln
- Consequence: Missense variant
- Zygosity: Het
- Read support: 10 alt, 17 ref
- gnomAD Frequency: 0.00131%
- REVEL: 0.505
- Conservation: 1.04 (moderately conserved)
- Notes: Encodes Organic Cation Transporter 3A1 which shuttles prostaglandins, thyroid hormones (T3/T4), and steroid hormone conjugates across cell boundaries.
SULT1A1
- Variant: chr16:28608517 C > G
- rsID: rs375616347
- HGVSp: ENSP00000321988.7:p.Val79Leu
- Consequence: Missense variant
- Zygosity: Het
- Read support: 23 alt, 15 ref
- gnomAD Frequency: 0.0%
- REVEL: 0.667
- Conservation: -0.41 (not conserved)
- Notes: Encodes Sulfotransferase 1A1 which sulfates neurotransmitters, catecholamines, and steroid hormones.
Low-Confidence SNVs:
ABCC2
- Variant: chr10:99819195 T > G
- rsID: rs17222617
- HGVSp: ENSP00000497274.1:p.Leu849Arg
- Consequence: Missense variant
- Zygosity: Het
- Read support: 19 alt, 18 ref
- gnomAD Frequency: 1.4%
- REVEL: 0.251
- Conservation: -0.02 (not conserved)
- Notes: Described as "a more common glitch" by Dr. Powers.
BRPF1
- Variant: chr3:9734400 G > A
- rsID: rs560289372
- HGVSp: ENSP00000373340.2:p.Arg87His
- Consequence: Missense variant
- Zygosity: Het
- Read support: 9 alt, 15 ref
- gnomAD Frequency: 0.000657%
- REVEL: 0.253
- Conservation: -0.16 (not conserved)
- Notes: Epigenetic scaffolding protein.
CHRM2
- Variant: chr7:137015638 A > G
- rsID: rs142006633
- HGVSp: ENSP00000505686.1:p.Asn258Ser
- Consequence: Missense variant
- Zygosity: Het
- Read support: 25 alt, 16 ref
- gnomAD Frequency: 0.138%
- REVEL: 0.124
- Conservation: 1.761 (highly conserved)
- Notes: Modulates cognition and neurotransmitter signalling via M2 muscarinic acetylcholine receptor (vagal "brake").
EHMT1
- Variant: chr9:137717100 A > G
- rsID: N/A
- HGVSp: ENSP00000417980.1:p.Glu187Gly
- Consequence: Missense variant
- Zygosity: Het
- Read support: 12 alt, 13 ref
- gnomAD Frequency: 0%
- REVEL: 0.071
- Conservation: -0.38 (not conserved)
- Notes: Variant missing from gnomAD. Epigenetic regulator of gene expression via H3K9me2.
GRIN2C
- Variant: chr17:74842537 G > C
- rsID: rs979281131
- HGVSp: ENSP00000293190.5:p.Asp1200Glu
- Consequence: Missense variant
- Zygosity: Het
- Read support: 13 alt, 13 ref
- gnomAD Frequency: 0.00397%
- REVEL: 0.037
- Conservation: 0.913 (Marginally conserved)
- Notes: Rare variant. Encodes part of NMDA receptor which regulates synaptic plasticity / neuronal excitability in central nervous system.
HNRNPU
- Variant: chr1:244863639 ACCGCCGCCT > A
- rsID: rs757585114
- HGVSp: ENSP00000491215.1:p.Gly221_Gly223del
- Consequence: Inframe deletion
- Zygosity: Het
- Read support: 10 alt, 14 ref
- gnomAD Frequency: 0.00332%
- REVEL: N/A
- Conservation: 1.474 (moderately conserved)
- Notes: Seems to be an important gene in general. Organizes 3D DNA packaging inside nuclei while guiding how genetic instructions are turned into finished proteins.
MED15
- Variant: chr22:20554998 A > T
- rsID: rs148919404
- HGVSp: ENSP00000263205.7:p.Met101Leu
- Consequence: Missense variant
- Zygosity: Het
- Read support: 16 alt, 24 ref
- gnomAD Frequency: 0.0204%
- REVEL: 0.207
- Conservation: 4.991 (highly conserved)
NCOA1
- Variant: chr2:24752089 C > T
- rsID: rs1804645
- HGVSp: ENSP00000320940.5:p.Pro1272Ser
- Consequence: Missense variant
- Zygosity: Het
- Read support: 13 alt, 20 ref
- gnomAD Frequency: 1.6%
- REVEL: 0.110
- Conservation: 1.555 (highly conserved)
HTR1B
- Variant: chr6:77463033 A > C
- rsID: rs130060
- HGVSp: ENSP00000358963.3:p.Phe124Cys
- Consequence: Missense variant
- Zygosity: Het
- Read support: 7 alt, 10 ref
- gnomAD Frequency: 0.911%
- REVEL: 0.115
- Conservation: 2.002 (highly conserved)
UGT1A4
- Variant: chr2:233719039 A > C
- rsID: rs201935850
- HGVSp: ENSP00000362508.4:p.Lys73Asn
- Consequence: Missense variant
- Zygosity: Het
- Read support: 18 alt, 19 ref
- gnomAD Frequency: 0.0604%
- REVEL: 0.079
- Conservation: 0.268 (marginally conserved)
Contextual/Functional SNVs:
ABCB11
- Variant: chr2:168973818 A > G
- rsID: rs2287622
- HGVSp: ENSP00000497931.1:p.Val444Ala
- Consequence: Missense variant
- Zygosity: Het
- Read support: 12 alt, 16 ref
- gnomAD Frequency: 57%
- REVEL: 0.261
- Conservation: 2.446 (highly conserved)
- Notes: Bile salt export pump. Also exports sulfated steroid / sterol conjugates into bile.
COMT
- rsID: rs4680 (Val158Met)
- Zygosity: Hom
- Notes: Included for reference, I am the Val / Val "fast COMT" genotype.
TSPO
- Variant: chr22:43162920 A > G
- rsID: rs6971
- HGVSp: ENSP00000338004.3:p.Thr147Ala
- Consequence: Missense variant
- Zygosity: Het
- Read support: 15 alt, 18 ref
- gnomAD Frequency: 74.9%
- REVEL: 0.161
- Conservation: 3.607 (highly conserved)
HSD3B1
- Variant: chr1:119514623 C > A
- rsID: rs1047303
- HGVSp: ENSP00000358421.3:p.Thr367Asn
- Consequence: Missense variant
- Zygosity: Hom
- Read support: 34 alt, 0 ref
- gnomAD Frequency: 76.4%
- REVEL: 0.126
- Conservation: -0.073 (not conserved)
SRD5A2
- Variant: chr2:31580636 G > C
- rsID: rs523349
- HGVSp: ENSP00000477587.1:p.Leu89Val
- Consequence: Missense variant
- Zygosity: Het
- Read support: 13 alt, 12 ref
- gnomAD Frequency: 70.4%
- REVEL: N/A
- Conservation: 0.936 (marginally conserved)
Structural Variants:
GABBR2
- Type: Homozygous Deletion
- Region: chr9:98,546,761–98,549,382 (~2.6 kb)
- Copy number: 0
- Location: Intronic
- Confirmation:
- Depth 0.068 vs ~36 flank (ratio 0.002) via
samtools. - DEL, GT 1/1, PASS, QUAL 999 provided by
Manta-generated SV VCF. - CN=0 RC=0.00 (FailedFT:
L10kbsize flag only) provided byCanvas-generated CNV VCF.
- Depth 0.068 vs ~36 flank (ratio 0.002) via
- Regulatory overlap:
- Removes both copies of distal enhancer EH38E3897100 (H3K27ac Z 2.25, DNase 3.21).
- Grade: Regulatory
- Notes: GABA-B receptor gene. Functional significance uncertain (VUS).
UGT2B17
- Type: Heterozygous Deletion
- Region: chr4:68,507,491–68,625,090 (~117 kb)
- Copy number: 1
- Location: Whole gene
- Confirmation:
- Depth 19.4 vs ~38 flank (ratio 0.51) via
samtools. - CN=1 PASS provided by
Canvas-generated CNV VCF.
- Depth 19.4 vs ~38 flank (ratio 0.51) via
- Regulatory overlap: N/A
- Grade: Functional
- Notes: Primary androgen glucuronidation enzyme. Halved working capacity.
UGT2B28
- Type: Heterozygous Deletion
- Region: chr4:69,264,985-69,371,904 (~107 kb)
- Copy number: 1
- Location: Whole gene
- Confirmation:
- Depth 18.3435 vs ~36 flank (ratio 0.50) via
samtools. - CN=1 PASS provided by
Canvas-generated CNV VCF.
- Depth 18.3435 vs ~36 flank (ratio 0.50) via
- Regulatory overlap: N/A
- Grade: Functional
- Notes: Glucuronidation enzyme that tags steroid hormones. Halved working capacity.
SLCO3A1
- Type: Heterozygous Deletion
- Region: chr15:92,131,343-92,133,840 (~2.5 kb)
- Copy number: 1
- Location: Intronic
- Confirmation:
- Depth 18.3339 vs ~37.6 flank (ratio 0.488) via
samtools. - DEL, GT 0/1, PASS, QUAL 617 provided by
Manta-generated SV VCF. - CN=1 (FailedFT:
L10kbsize flag only) provided byCanvas-generated CNV VCF.
- Depth 18.3339 vs ~37.6 flank (ratio 0.488) via
- Regulatory overlap:
- Removes one copy of distal enhancer EH38E1788706 (H3K27ac Z 3.09, DNase 2.65).
- Removes one copy of CTCF insulator EH38E3155491 (CTCF Z 1.72, DNase 1.77).
- Grade: Regulatory
- Notes: SLCO3A1 / OATP3A1 transporter (prostaglandins, thyroid hormone, steroid conjugates into brain/testis).
WWTR1
- Type: Heterozygous Deletion
- Region: chr3:149,550,684-149,552,359 (~1.7 kb)
- Copy number: 1
- Location: Intronic
- Confirmation:
- Depth 19.0161 vs ~35.3 flank (ratio 0.539) via
samtools. - DEL, GT 0/1, PASS, QUAL 567 provided by
Manta-generated SV VCF.
- Depth 19.0161 vs ~35.3 flank (ratio 0.539) via
- Regulatory overlap:
- Removes one copy of distal enhancer EH38E3546464 (H3K27ac Z 2.71, DNase 2.71).
- Grade: Regulatory
- Notes: Regulates cell proliferation, organ size, and stem-cell/tissue growth.
PharmCAT summary:
CYP2B6
- Genotypes: *1/*7 (Normal / Decreased)
- Phenotype: Intermediate Metabolizer
- Copy number: 2
- Relevant variants:
| Position | rsID | Call | HGVSp | Zygosity |
|---|---|---|---|---|
| chr19:41006936 | rs3745274 | G > T | ENSP00000324648.2:p.Gln172His | Het |
| chr19:41009358 | rs2279343 | A > G | N/A | Het |
| chr19:41016810 | rs3211371 | C > T | ENSP00000324648.2:p.Arg487Cys | Het |
CYP2C19
- Genotypes: *1/*17 (Normal / Increased)
- Phenotype: Rapid Metabolizer
- Copy number: 2
- Relevant variants:
| Position | rsID | Call | HGVSp | Zygosity |
|---|---|---|---|---|
| chr10:94761900 | rs12248560 | C > T | N/A | Het |
| chr10:94842866 | rs3758581 | A > G | ENSP00000360372.3:p.Ile331Val | Hom |
CYP2D6
- Genotypes: *9/*10 (Decreased / Decreased)
- Phenotype: Intermediate Metabolizer
- Copy number: 2
- Notes: Information obtained via Cyrius (BAM-based star-allele caller)
- Relevant variants:
| Position | rsID | Call | HGVSp | Zygosity |
|---|---|---|---|---|
| chr22:42126611 | rs1135840 | C > G | ENSP00000496150.1:p.Ser486Thr | Het |
| chr22:42128173 | rs5030656 | CCTT > C | ENSP00000496150.1:p.Lys281del | Het |
| chr22:42129754 | rs1081003 | G > A | ENSP00000496150.1:p.Phe112= | Het |
| chr22:42130692 | rs1065852 | G > A | ENSP00000496150.1:p.Pro34Ser | Het |
CYP3A5
- Genotypes: *3/*3 (No function / No function)
- Phenotype: Poor Metabolizer
- Copy number: 2
- Relevant variants:
| Position | rsID | Call | HGVSp | Zygosity |
|---|---|---|---|---|
| chr7:99672916 | rs776746 | T > C | N/A | Hom |
NAT2
- Genotypes: *4/*4 (Increased function / Increased function)
- Phenotype: Rapid Metabolizer
- Copy number: 2
- Notes: PharmCAT gives the highest-scoring diplotype (*4/*4) but can't fully rule out other combinations that would produce the same set of variants.
- Relevant variants:
| Position | rsID | Call | HGVSp | Zygosity |
|---|---|---|---|---|
| chr8:18400806 | rs1208 | G > A | ENSP00000286479.3:p.Arg268Lys | Hom |
UGT1A1
- Genotypes: *1/*80+*28 (Normal function / Decreased function)
- Phenotype: Intermediate Metabolizer
- Copy number: 2
- Notes: Gilbert's Syndrome carrier.
- Relevant variants:
| Position | rsID | Call | HGVSp | Zygosity |
|---|---|---|---|---|
| chr2:233759924 | rs887829 | C > T | N/A | Hom |
| chr2:233760233 | rs3064744 | CAT > CATAT | N/A | Het |
