Couldn't find variants for GPR179 gene

[AlessandroLas]

Dear all,

I could not find any variants in the GPR179 gene (screenshot 1).
I searched by basic filtering (eg: removing SNPs and scrolling the results) and by Location filtering (using the gene symbol).
I double checked that the VCF has variants in that gene.
However, if I search by using its ENSG (ENSG00000188888) or by its coordinates (hg19, chr17:36480454-36499839),
I could find the variants I was looking for in a gene called GPR179 (screenshot 2)

After checking I noticed that I'm experiencing this issue in all the projects.

can you help?
Thanks.

Screenshot 1

Screenshot 2

[hanars]

When you click into the gene info shown on the variant, can you confirm what Ensembl ID is associated with the gene?

[AlessandroLas]

Hi Hana.
It says ENSG00000188888

[hanars]

Thank you. Can you please provide the elasticsearch and seqr logs for the gene search that is not returning results? Please make sure to reset your redis cache before rerunning the search

[AlessandroLas]

Thanks for the prompt reply.

I'm not sure of how many rows should I paste here below...
However, I ran

docker-compose exec -i redis redis-cli FLUSHALL

docker-compose logs --tail 20 elasticsearch
elasticsearch | {"type": "server", "timestamp": "2025-02-10T11:24:29,576Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][609074] overhead, spent [876ms] collecting in the last [1.4s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T11:25:09,988Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][609114] overhead, spent [862ms] collecting in the last [1.3s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T11:57:17,872Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][young][611040][75507] duration [1.2s], collections [1]/[1.8s], total [1.2s]/[44.1m], memory [10.8gb]->[8.2gb]/[15gb], all_pools {[young] [3.8gb]->[0b]/[0b]}{[old] [6.8gb]->[7.7gb]/[15gb]}{[survivor] [132.6mb]->[560mb]/[0b]}", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T11:57:17,872Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][611040] overhead, spent [1.2s] collecting in the last [1.8s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T11:58:35,950Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][611118] overhead, spent [576ms] collecting in the last [1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T12:04:58,498Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][611500] overhead, spent [739ms] collecting in the last [1.3s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T12:54:47,101Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][young][614486][75907] duration [1.1s], collections [1]/[1.5s], total [1.1s]/[44.4m], memory [11gb]->[7.9gb]/[15gb], all_pools {[young] [4gb]->[0b]/[0b]}{[old] [6.8gb]->[7.4gb]/[15gb]}{[survivor] [134.6mb]->[560mb]/[0b]}", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T12:54:47,102Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][614486] overhead, spent [1.1s] collecting in the last [1.5s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T12:58:51,191Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][614730] overhead, spent [890ms] collecting in the last [1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T13:55:21,113Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][618116] overhead, spent [570ms] collecting in the last [1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T14:27:29,600Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][620042] overhead, spent [859ms] collecting in the last [1.1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T14:43:09,054Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][620981] overhead, spent [903ms] collecting in the last [1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T14:55:00,668Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][young][621692][76727] duration [1s], collections [1]/[1.2s], total [1s]/[44.9m], memory [10.8gb]->[8.1gb]/[15gb], all_pools {[young] [3.7gb]->[0b]/[0b]}{[old] [6.8gb]->[7.5gb]/[15gb]}{[survivor] [227.3mb]->[552mb]/[0b]}", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T14:55:00,669Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][621692] overhead, spent [1s] collecting in the last [1.2s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T14:55:01,669Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][621693] overhead, spent [522ms] collecting in the last [1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T14:59:50,337Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][621981] overhead, spent [787ms] collecting in the last [1.5s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T14:59:51,337Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][621982] overhead, spent [538ms] collecting in the last [1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T15:00:56,636Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][622047] overhead, spent [731ms] collecting in the last [1.2s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T15:05:36,772Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][622327] overhead, spent [891ms] collecting in the last [1s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }
elasticsearch | {"type": "server", "timestamp": "2025-02-10T15:29:16,929Z", "level": "WARN", "component": "o.e.m.j.JvmGcMonitorService", "cluster.name": "es-docker-cluster", "node.name": "elasticsearch", "message": "[gc][623746] overhead, spent [765ms] collecting in the last [1.3s]", "cluster.uuid": "EZ1VheqkSSmDytmcg4PYGQ", "node.id": "iYd0jSD4Q2OWGMGgF_KVTg" }

docker-compose logs --tail 20 seqr
seqr-seqr-1 | {"timestamp": "2025-02-10 15:29:41,154", "severity": "INFO", "httpRequest": {"requestMethod": "GET", "requestUrl": "https://vareval.ceinge.unina.it/api/data_management/elasticsearch_status", "status": 200, "responseSize": 4377422, "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36", "remoteIp": "192.168.228.12", "referer": "https://vareval.ceinge.unina.it/data_management/elasticsearch_status", "protocol": "HTTP/1.1"}, "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:31:42,976", "severity": "INFO", "message": "create VariantSearchResults VSR0040115_ac69a94f7b7447587d5", "user": "lasorsa@ceinge.unina.it", "dbUpdate": {"dbEntity": "VariantSearchResults", "entityId": "VSR0040115_ac69a94f7b7447587d5", "updateType": "create", "updateFields": ["search_hash", "variant_search"]}}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:31:43,068", "severity": "INFO", "message": "GET http://elasticsearch:9200/gr23184/_mapping [status:200 request:0.003s]"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:31:43,073", "severity": "INFO", "message": "Searching in elasticsearch indices: gr23184", "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:31:43,073", "severity": "INFO", "message": "Loading gr23184 records 0-100", "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:31:43,078", "severity": "INFO", "message": "POST http://elasticsearch:9200/gr23184/_search [status:200 request:0.005s]"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:31:43,079", "severity": "INFO", "message": "Total hits: 0 (0.003 seconds)", "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:31:43,084", "severity": "INFO", "httpRequest": {"requestMethod": "POST", "requestUrl": "https://vareval.ceinge.unina.it/api/search/ac69a94f7b7447587d5467b10a786e20?sort=pathogenicity&page=1&loadFamilyContext=false&loadProjectTagTypes=false", "status": 200, "responseSize": 394, "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36", "remoteIp": "192.168.228.12", "referer": "https://vareval.ceinge.unina.it/variant_search/results/ac69a94f7b7447587d5467b10a786e20?page=1&sort=pathogenicity", "protocol": "HTTP/1.1"}, "requestBody": {"projectFamilies": [{"familyGuids": ["F007642_gr23184"], "projectGuid": "R0042_wgs_iolascon"}], "search": {"locus": {"rawItems": "GPR179"}}, "totalResults": 0}, "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:33:23,357", "severity": "INFO", "httpRequest": {"requestMethod": "GET", "requestUrl": "https://vareval.ceinge.unina.it/", "status": 200, "responseSize": 1751, "userAgent": "Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/132.0.0.0 Safari/537.36", "remoteIp": "192.168.228.116", "referer": null, "protocol": "HTTP/1.1"}, "user": "tirelli@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:11,334", "severity": "INFO", "httpRequest": {"requestMethod": "GET", "requestUrl": "https://vareval.ceinge.unina.it/api/family/F007641_aner2024_00223/details", "status": 200, "responseSize": 4431, "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36", "remoteIp": "192.168.228.12", "referer": "https://vareval.ceinge.unina.it/project/R0042_wgs_iolascon/family_page/F007641_aner2024_00223", "protocol": "HTTP/1.1"}, "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:11,392", "severity": "INFO", "httpRequest": {"requestMethod": "GET", "requestUrl": "https://vareval.ceinge.unina.it/api/family/F007641_aner2024_00223/details", "status": 200, "responseSize": 4431, "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36", "remoteIp": "192.168.228.12", "referer": "https://vareval.ceinge.unina.it/project/R0042_wgs_iolascon/family_page/F007641_aner2024_00223", "protocol": "HTTP/1.1"}, "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:13,416", "severity": "INFO", "httpRequest": {"requestMethod": "POST", "requestUrl": "https://vareval.ceinge.unina.it/api/search_context", "status": 200, "responseSize": 21266, "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36", "remoteIp": "192.168.228.12", "referer": "https://vareval.ceinge.unina.it/variant_search/family/F007641_aner2024_00223", "protocol": "HTTP/1.1"}, "requestBody": {"projectGuid": "R0042_wgs_iolascon"}, "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:13,812", "severity": "INFO", "httpRequest": {"requestMethod": "GET", "requestUrl": "https://vareval.ceinge.unina.it/api/all_locus_list_options", "status": 200, "responseSize": 520924, "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36", "remoteIp": "192.168.228.12", "referer": "https://vareval.ceinge.unina.it/variant_search/family/F007641_aner2024_00223", "protocol": "HTTP/1.1"}, "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:30,680", "severity": "INFO", "message": "create VariantSearchResults VSR0040116_28fa175df5ba74270f6", "user": "lasorsa@ceinge.unina.it", "dbUpdate": {"dbEntity": "VariantSearchResults", "entityId": "VSR0040116_28fa175df5ba74270f6", "updateType": "create", "updateFields": ["search_hash", "variant_search"]}}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:30,769", "severity": "INFO", "message": "GET http://elasticsearch:9200/aner2024_00223/_mapping [status:200 request:0.003s]"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:30,772", "severity": "INFO", "message": "Searching in elasticsearch indices: aner2024_00223", "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:30,772", "severity": "INFO", "message": "Loading aner2024_00223 records 0-100", "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:30,776", "severity": "INFO", "message": "POST http://elasticsearch:9200/aner2024_00223/_search [status:200 request:0.003s]"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:30,776", "severity": "INFO", "message": "Total hits: 0 (0.001 seconds)", "user": "lasorsa@ceinge.unina.it"}
seqr-seqr-1 | {"timestamp": "2025-02-10 15:35:30,781", "severity": "INFO", "httpRequest": {"requestMethod": "POST", "requestUrl": "https://vareval.ceinge.unina.it/api/search/28fa175df5ba74270f61f4aebba29db3?sort=pathogenicity&page=1&loadFamilyContext=false&loadProjectTagTypes=false", "status": 200, "responseSize": 401, "userAgent": "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_7) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/130.0.0.0 Safari/537.36", "remoteIp": "192.168.228.12", "referer": "https://vareval.ceinge.unina.it/variant_search/results/28fa175df5ba74270f61f4aebba29db3?page=1&sort=pathogenicity", "protocol": "HTTP/1.1"}, "requestBody": {"projectFamilies": [{"projectGuid": "R0042_wgs_iolascon", "familyGuids": ["F007641_aner2024_00223"]}], "search": {"locus": {"rawItems": "GPR179"}}}, "user": "lasorsa@ceinge.unina.it"}

[hanars]

Can you provide the more recent elasticsearch logs? the last log you include is timstamped 15:29:16, which is before the corresponding seqr log for the elasticsearch search at 15:31:43 . Also, could you run seqr with the log level set to DEBUG, and include search logs for that as well?