Gene: VHL (HGNC:12687)
Evidence Code: PVS1 — Very Strong
Modification Type: Disease-specific,General recommendation
LINK TO PVS1 DECISION TREE DOCUMENT:
 
https://drive.google.com/file/d/1mGfChgxbGVbzYn6Ggmb9rYvoGGah25ll/view?usp=sharing


Do not apply PVS1 for truncations that occur prior to Codon 54 (including frameshift events that start and end prior to Codon 54 but the truncation extends beyond Codon 54.)


Note1: Exon presence in biologically relevant transcripts:
 In some transcripts exon 2 of 
VHL
 is skipped and expressed at low levels. The function of this transcript is not fully known. Exon 2 comprises almost the entirety of the nuclear export function region of the Beta domain and is critical for known VHL function. Exon 1 contains the only initiator codons in 
VHL
. Exon 3 contains the elongin binding function. 
All exons should be considered as "present in biologically relevant transcripts" in the PVS1 decision tree.


Note 2: The 10% PVS1 downgrade to Moderate cannot apply to VHL
 because of the small size.


Nonsense Mediated Decay
 
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NMD experimental evidence in 1st exon after codon 54 and to 5' region of 2nd exon (codon 138)
.**


Critical Domains:


1st Beta (β) domain (63-154), especially Nuclear Export (114-155)


Alpha (ɑ) domain (155-192), especially Elongin C binding (157 - 172)


Second Beta domain (193-204)   


Truncating variants after Met54 and predicted to undergo NMD (from AA55-AA136/c.408) or in the beta or alpha domains can receive PVS1, and those outside the second Beta domain (205-213) can receive PVS1_Moderate downgrade to account for minimal loss of VHL protein. Notably a frame shift deletion at 205 is pathogenic in ClinVar (ID 18971) as are stop loss extension variants in the last codons (see PM4).


SPLICE: If any canonical exon is skipped, the variant receives PVS1.
 If a cryptic splice disrupts the reading frame, and is in a critical domain (AA63-AA204) or is predicted to undergo NMD (AA55-AA136) it receives PVS1. If it is outside a critical domain and predicted to undergo NMD (AA55-62), it receives PVS1_Strong (the second site outside of critical domains AA205-213 is not predicted to undergo NMD). If a cryptic splice does not alter the reading frame, and is in a critical domain (AA 63-204), it can receive PVS1_Strong, and if it is outside the critical domain (AA 205-213) or  in an NMD prediction (AA 55-62), it receives PVS1_Moderate. Note:  There is a cryptic exon (E1) in intron 1 
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6
, and silent variants in exon 2 that are reported to cause skipping of exon 1. If there is functional evidence of exon skipping (RNA splice assay) then PVS1 can apply. Do not double count evidence. Ex. PVS1 should be used in place of PS3 functional evidence confirming splice alteration, but PS3 evidence code could still apply to other relevant assays confirming effect on HIF1/2a presence etc. 


EXON DELETION:
 SVI PVS1 decision tree modified for whole exon deletions. There are only 3 exons in 
VHL
 and each has an important functional domain. Any exon deletion of 
VHL
 receives PVS1. 


EXON DUPLICATION:
 Follow PVS1 decision tree. Note: few pathogenic exon duplications are reported in ClinVar.   (ID:417571, ID:584137). These have no literature cited. 


INITIATION CODON:
 VHL Met 1 (in VHL p30) truncation or missense would not affect VHL p19, as VHL has a second start at codon 54 (VHL p19), it cannot be scored in the PVS1 decision tree. After that, no other viable alternative starts are known. Start loss at codon 54 would presumably result in an impact, as VHL p30 and p19 would be truncated prior to any known functional domains (PVS1). Ong 2007 has 1 family (2 subjects) with Met54X and reports cerebellar hemangioblastomas. There is no functional study in the paper for this variant. Olschwang et al 1998 VHL Type 2A, one subject with 161insT (FS result). There is no functional study in the paper. Missense at Met 54 (VHL p19 initiation codon) would presumably not result in as strong an impact as the full length VHL p30 would still be produced (PVS1 decision tree = N/A). ClinVar has M54T (ID:819688) and M54L (ID:843990). M54T is uncertain, with no other evidence provided. M54L references M54I which segregates in homozygous state with erythrocytosis in individuals of Moroccan descent 
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, and those heterozygous for M54I did not present VHL phenotype 
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.