ANO5 Gene has associated diseases in HPO database, but not in exomiser output

[ccbruels]

Hi, we have 2 variants in the ANO5 gene that are P/LP, but the gene has an extremely low exomiser ranking.

There are 7 diseases associated with ANO5 in the HPO terms (https://hpo.jax.org/browse/gene/NCBIGene:203859).

The exomiser output shows no phenotype or disease associations for ANO5, which I think is the reason for the low exomiser rank.
ANO5-NoDiseaseAssnExomiser.docx

The variants in ANO5 also have no disease ID or disease name in the exomiser output files variants.tsv or the vcf.gz.

137-1
1381 11-22270378-G-C_AD ANO5 102723370 AD 0.6511 0.0004 0.0000 0.9971 0.9971 1 0 rs760137559 11 22270378 22270378 G C 0 50.3500 PASS 0|1 missense_variant ANO5:ENST00000324559.9:c.1965G>C:p.(Trp655Cys) UNCERTAIN_SIGNIFICANCE PM5,PP3_Moderate,BP1 523571 CONFLICTING_PATHOGENICITY_INTERPRETATIONS 1 0.86736 0.73 1.035 GNOMAD_G_NFE 0.0014699397 GNOMAD_E_NFE=8.992951E-5,GNOMAD_E_SAS=0.0011593128,GNOMAD_G_NFE=0.0014699397 ALPHA_MISSENSE 0.9973 REVEL=0.776,MVP=0.70669335,ALPHA_MISSENSE=0.9973

1467-1
1060 11-22257706-C-G_AD ANO5 102723370 AD 0.5688 0.0010 0.0000 1.0000 1.0000 1 1 rs754889480 11 22257706 22257706 C G 0 54.6600 PASS 1|0 stop_gained ANO5:ENST00000324559.9:c.1359C>G:p.(Tyr453*) UNCERTAIN_SIGNIFICANCE PP5_Strong 694040 PATHOGENIC 2 0.86736 0.73 1.035 GNOMAD_E_AMR 0.0022366361 GNOMAD_E_AMR=0.0022366361

The ANO5 gene is in the HPO terms included in the .yml files. The variants are only shown withe the FULL analysis option, and then filtering based on the gene name.

Is this an issue within exomiser?

[pnrobinson]

Are you able to share the HPO terms you used for the analysis or at least the count of terms and which of the three ANO5-associated diseases is deemed to be the correct diagnosis?

[ccbruels]

Hi, We frequently don't have detailed histories available, so we start with hpoIds: [ 'HP:0011805', 'HP:0011804' ] to cast a broader net, then narrow the hpo list based on what we do know. In these two specfic cases, we didn't see the clinically identified variants (both had ANO5 hets, one also had a PYGM het) so we also tried hpoIds: [ 'HP:0003560', 'HP:0003198' ] #md and myopathy and hpoIds: [ 'HP:0001324' ] # muscle weakness. Since we still weren't seeing the ANO5 or PYGM variants, for the full analysis I used hpoIds: [ 'HP:0003560', 'HP:0003201', 'HP:0003202' ] # md, elev ck, rhabdo. My concern is that there are clearly related muscle diseases associated with ANO5 , yet the exomiser disease fields were empty, likely leading to the low exomiser score. Best, Christine

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On Thu, Apr 9, 2026 at 12:39 AM Peter Robinson ***@***.***> wrote: *pnrobinson* left a comment (exomiser/Exomiser#637) <#637 (comment)> Are you able to share the HPO terms you used for the analysis or at least the count of terms and which of the three ANO5-associated diseases is deemed to be the correct diagnosis? — Reply to this email directly, view it on GitHub <#637 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIZPTZXBKWBTS5JRDFUUHYL4U4ZRXAVCNFSM6AAAAACXRT5GCWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DEMJRGY4TSOJXGI> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[pnrobinson]

Thanks!
In principle, those HPO terms should have at least some match (https://hpo.jax.org/browse/gene/NCBIGene:203859), and if the variant is either ClinVar P/LP or bioinformatics-pathogenic, then the disease should have a decent rank. @julesjacobsen any ideas how to troubleshoot this?

[julesjacobsen]

Are these two variants from two different cases? The variants are heterozygous whereas the muscular dystrophies linked to ANO5 in the Exomiser phenotype database (2512) are both recessive:

OMIM:611307 AR Muscular dystrophy, limb-girdle, autosomal recessive 12
OMIM:613319 AR Miyoshi muscular dystrophy 3
ORPHA:206549 AR Anoctamin-5-related limb-girdle muscular dystrophy R12

They would both need to be present in the same case to fit an autosomal recessive compound heterozygous pattern. The only AD disorders are:

OMIM:166260 AD Gnathodiaphyseal dysplasia
ORPHA:206599 AD Isolated asymptomatic elevation of creatine phosphokinase
ORPHA:53697 AD Gnathodiaphyseal dysplasia

Elevated circulating creatine kinase concentration is HP:0003236 not HP:0003202 (Skeletal muscle atrophy), so this would explain your lack of a good score.

Using:
ano5.vcf.txt
ano5-phenopacket.yml.txt

With:

java -Dexomiser.hg38.data-version=2512 -Dexomiser.phenotype.data-version=2512 -jar exomiser-cli-15.0.0.jar analyse --sample ano5-phenopacket.yml.txt --vcf ano5.vcf.txt --assembly hg38

Produces:
ano5-exomiser.html

Gene Symbol	MOI	Gene Identifier	Gene Name	Exomiser Score	Phenotype Score	Variant Score	Exomiser ACMG	ClinVar ACMG
ANO5	AD	HGNC:27337	ENSG00000171714	0.841 p=3.0E-5	0.851	1.000	LIKELY PATHOGENIC	PATHOGENIC

What are the settings and data versions you're using for the analysis?

[ccbruels]

Hi Jules, Thanks so much for your reply! The two variants were from different cases. We are frequently looking for additional variants that were missed on clinical testing, so it's helpful to have hets scored even when the gene/disease is recessive. You're correct about the HPO for elevated CK, I copied the wrong HPO into my email, apologies. I noticed that your command included exomiser-cli-15.1.0 jar, but the most recent available version is 15.0. When I ran: java -Dexomiser.hg38.data-version=2512 -Dexomiser.phenotype.data-version=2512 -jar exomiser-cli-15.0.0.jar analyse --sample ano5-phenopacket.yml.txt --vcf ano5.vcf.txt --assembly hg38 I got the attached html that still shows the AD variant score of 1.0 but no ANO5 associated disorders or ANO5 phenotype matches. I think my phenotype data is correct: ***@***.***:/projects/standard/pkang/shared/software/exomiser-cli-15.0.0$ ls -lt data/2512_phenotype/phenix/ total 11761 -rwxrwx---. 1 ccbruels pkang 5849718 Nov 5 04:28 ALL_SOURCES_ALL_FREQUENCIES_genes_to_phenotype.txt -rwxrwx---. 1 ccbruels pkang 6192170 Nov 5 04:28 hp.obo drwxrws---. 2 ccbruels pkang 4096 Nov 5 04:28 out ***@***.***:/projects/standard/pkang/shared/software/exomiser-cli-15.0.0$ ls -lt data/2512_phenotype/ total 21981230 -rwxrwx---. 1 ccbruels pkang 21757693952 Nov 6 07:36 2512_phenotype.mv.db drwxrws---. 2 ccbruels pkang 4096 Nov 5 04:28 phenix -rwxrwx---. 1 ccbruels pkang 740933632 Nov 5 04:28 rw_string_10.mv -rwxrwx---. 1 ccbruels pkang 10151040 Nov 5 04:28 hp.obo Is it possible this is due to a difference between v.15.0.0 and 15.1.0? If so, when will 15.1.0 be available? Thank you so much for your help! [ano5.txt-exomiser.html](https://github.com/user-attachments/files/26800540/ano5.txt-exomiser.html) Best, Christine

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On Tue, Apr 14, 2026 at 2:27 PM Jules Jacobsen ***@***.***> wrote: *julesjacobsen* left a comment (exomiser/Exomiser#637) <#637 (comment)> Are these two variants from two different cases? The variants are heterozygous whereas the muscular dystrophies linked to ANO5 in the Exomiser phenotype database (2512) are both recessive: OMIM:611307 AR Muscular dystrophy, limb-girdle, autosomal recessive 12 OMIM:613319 AR Miyoshi muscular dystrophy 3 ORPHA:206549 AR Anoctamin-5-related limb-girdle muscular dystrophy R12 They would both need to be present in the same case to fit an autosomal recessive compound heterozygous pattern. The only AD disorders are: OMIM:166260 AD Gnathodiaphyseal dysplasia ORPHA:206599 AD Isolated asymptomatic elevation of creatine phosphokinase ORPHA:53697 AD Gnathodiaphyseal dysplasia Elevated circulating creatine kinase concentration is HP:0003236 <https://hpo.jax.org/browse/term/HP:0003236> not HP:0003202 <https://hpo.jax.org/browse/term/HP:0003202> (Skeletal muscle atrophy), so this would explain your lack of a good score. Using: ano5.vcf.txt <https://github.com/user-attachments/files/26724137/ano5.vcf.txt> ano5-phenopacket.yml.txt <https://github.com/user-attachments/files/26724192/ano5-phenopacket.yml.txt> With: java -Dexomiser.hg38.data-version=2512 -Dexomiser.phenotype.data-version=2512 -jar exomiser-cli-15.1.0.jar analyse --sample ano5-phenopacket.yml.txt --vcf ano5.vcf.txt --assembly hg38 Produces: ano5-exomiser.html <https://github.com/user-attachments/files/26724223/ano5-exomiser.html> What are the settings you're using for the analysis? — Reply to this email directly, view it on GitHub <#637 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIZPTZRLZOON2KBPFNRU7ED4V2GIXAVCNFSM6AAAAACXRT5GCWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DENBWGU3TENBWGE> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[julesjacobsen]

Are you sure you're looking at the correct output file? It's nothing to do with a 15/15.1 difference.

15.1.0 will be out once we've finished testing, which might be a couple of weeks.

[ccbruels]

I ran this job thru our slurm scheduler, from the exomiser directory, with the same command you used and the yml and vcf you posted (java -Dexomiser.hg38.data-version=2512 -Dexomiser.phenotype.data-version=2512 -jar exomiser-cli-15.0.0.jar analyse --sample ano5-phenopacket.yml.txt --vcf ano5.vcf.txt --assembly hg38). The output was in the exomiser results directory, and I attached the html file previously. AFAICT, I am looking at the correct output file. It is timestamped at the time that the job completed, it's in the exomiser install results directory, not our sample results directory tree. The settings show that it used the expected vcf (from your previous post) and the same HPOs that you used. Our HPC slurm scheduler is having a bad monday lol, so I am unable to rerun that same analysis with the output going to a specified location and name, but I'm as certain as I can be that I viewed and attached the correct output file. I can't see that there is anything different between our analyses, except the exomiser version. Or possibly our data files didn't download correctly, which is why I included a screenshot of the files and sizes on our hpc. I checked a handful of genes in the full analysis that had a phenotype score of 0.000, they had associated disorders and phenotype matches, but a low score because they didn't match the input HPOs. Other genes are annotated with associated disorders and phenotype matches. I did notice that your output includes a Hugo gene name, while ours does not. But all of the genes in our output don't have a Hugo gene name, ANO5 is the only one I noticed on a cursory review that does not have the disorder or pheonotype matches. Puzzling... Best, Christine

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On Mon, Apr 20, 2026 at 11:48 AM Jules Jacobsen ***@***.***> wrote: *julesjacobsen* left a comment (exomiser/Exomiser#637) <#637 (comment)> Are you sure you're looking at the correct output file? It's nothing to do with a 15/15.1 difference. 15.1.0 will be out once we've finished testing, which might be a couple of weeks. — Reply to this email directly, view it on GitHub <#637?email_source=notifications&email_token=AIZPTZUU2UADOXIOTCONZPT4WZIENA5CNFSNUABFM5UWIORPF5TWS5BNNB2WEL2JONZXKZKDN5WW2ZLOOQXTIMRYGI3DONBRGE22M4TFMFZW63VGMF2XI2DPOKSWK5TFNZ2KYZTPN52GK4S7MNWGSY3L#issuecomment-4282674115>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIZPTZXCV4LNHSHJU4FX4FL4WZIENAVCNFSM6AAAAACXRT5GCWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DEOBSGY3TIMJRGU> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[julesjacobsen]

This is indeed puzzling. I'm not sure what to make of it. The only thing I can think of is that the application.properties might be pointing to an exomiser.data-directory where some different 2512 data resides, or your HPC was having an off day and you could try re-running things. The most likely explanation is that your 2512_phenotype data is corrupted, so you could try re-downloading and extracting.

[ccbruels]

Hi Jules, I finally circled back to this. With v15.0.0, I downloaded the phenotype data again as both https://data.monarchinitiative.org/exomiser/data/2512_phenotype.zip and https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2512_phenotype.zip. I verified that the application.properties was pointing to the correct exomiser.data-directory, For each download, I ran the command 2 ways just in case something was specified incorrectly for our system. I ran java -Dexomiser.hg38.data-version=2512 -Dexomiser.phenotype.data-version=2512 -jar exomiser-cli-15.0.0.jar analyse --sample ano5-phenopacket.yml.txt --vcf ano5.vcf.txt --assembly hg38, and also java -jar exomiser-cli-15.0.0.jar analyse --sample ano5-phenopacket.yml.txt --vcf ano5.vcf.txt --assembly hg38 . Both had the same result, the variant is annotated, has a variant score = 1 but phenotype score = 0 with no phenotype matches or associated disorders. I also did a clean install of v15.1.0. I only downloaded the data from https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2512_phenotype.zip (not the monarch site). I verified that all data locations were correctly specified, but had the same result. Is it possible that both of the phenotype data files ( https://data.monarchinitiative.org/exomiser/data/2512_phenotype.zip and https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2512_phenotype.zip) have some sort of error and that you are using a different version that does not have an error? I still haven't noticed any other genes having this issue. My concern is that we will miss something important because I haven't noticed the lack of phenotype matches. I don't have the tools to inspect the database files directly. Thanks so much for all of your help. AND for including the CADD phred scores in the html file! Best, Christine

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On Tue, May 5, 2026 at 5:43 AM Jules Jacobsen ***@***.***> wrote: *julesjacobsen* left a comment (exomiser/Exomiser#637) <#637 (comment)> This is indeed puzzling. I'm not sure what to make of it. The only thing I can think of is that the application.properties might be pointing to an exomiser.data-directory where some different 2512 data resides, or your HPC was having an off day and you could try re-running things. The most likely explanation is that your 2512_phenotype data is corrupted, so you could try re-downloading and extracting. — Reply to this email directly, view it on GitHub <#637 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIZPTZXXAPBSFO7XWOUW7334ZHAWZAVCNFSM6AAAAACXRT5GCWVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHM2DGNZYGUYTCNZWG4> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[ccbruels]

Hi,

Have you had a chance to look into the phenotype data files (https://data.monarchinitiative.org/exomiser/data/2512_phenotype.zip and
https://g-879a9f.f5dc97.75bc.dn.glob.us/data/2512_phenotype.zip) to see whether there is an issue with the files as posted? That seems the most likely source of this issue, since I've done clean installs of version 15.1.0 and the databases, and the error persists.

Thanks!
Christine