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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 3-193667167-CAGTT-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=193667167&ref=CAGTT&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 193667167,
"ref": "CAGTT",
"alt": "C",
"effect": "frameshift_variant,splice_region_variant",
"transcript": "NM_130837.3",
"consequences": [
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2873_2876delTTAG",
"hgvs_p": "p.Val958fs",
"transcript": "NM_130837.3",
"protein_id": "NP_570850.2",
"transcript_support_level": null,
"aa_start": 958,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2873,
"cds_end": null,
"cds_length": 3048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000361510.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130837.3"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2873_2876delTTAG",
"hgvs_p": "p.Val958fs",
"transcript": "ENST00000361510.8",
"protein_id": "ENSP00000355324.2",
"transcript_support_level": 5,
"aa_start": 958,
"aa_end": null,
"aa_length": 1015,
"cds_start": 2873,
"cds_end": null,
"cds_length": 3048,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_130837.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361510.8"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2819_2822delTTAG",
"hgvs_p": "p.Val940fs",
"transcript": "ENST00000361908.8",
"protein_id": "ENSP00000354681.3",
"transcript_support_level": 1,
"aa_start": 940,
"aa_end": null,
"aa_length": 997,
"cds_start": 2819,
"cds_end": null,
"cds_length": 2994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361908.8"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2888_2891delTTAG",
"hgvs_p": "p.Val963fs",
"transcript": "ENST00000968586.1",
"protein_id": "ENSP00000638645.1",
"transcript_support_level": null,
"aa_start": 963,
"aa_end": null,
"aa_length": 1020,
"cds_start": 2888,
"cds_end": null,
"cds_length": 3063,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968586.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2834_2837delTTAG",
"hgvs_p": "p.Val945fs",
"transcript": "ENST00000968584.1",
"protein_id": "ENSP00000638643.1",
"transcript_support_level": null,
"aa_start": 945,
"aa_end": null,
"aa_length": 1002,
"cds_start": 2834,
"cds_end": null,
"cds_length": 3009,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968584.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2819_2822delTTAG",
"hgvs_p": "p.Val940fs",
"transcript": "NM_130836.3",
"protein_id": "NP_570849.2",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 997,
"cds_start": 2819,
"cds_end": null,
"cds_length": 2994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130836.3"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2819_2822delTTAG",
"hgvs_p": "p.Val940fs",
"transcript": "ENST00000890753.1",
"protein_id": "ENSP00000560812.1",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 997,
"cds_start": 2819,
"cds_end": null,
"cds_length": 2994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890753.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2819_2822delTTAG",
"hgvs_p": "p.Val940fs",
"transcript": "ENST00000925500.1",
"protein_id": "ENSP00000595559.1",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 997,
"cds_start": 2819,
"cds_end": null,
"cds_length": 2994,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000925500.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2765_2768delTTAG",
"hgvs_p": "p.Val922fs",
"transcript": "NM_130835.3",
"protein_id": "NP_570848.1",
"transcript_support_level": null,
"aa_start": 922,
"aa_end": null,
"aa_length": 979,
"cds_start": 2765,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130835.3"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2765_2768delTTAG",
"hgvs_p": "p.Val922fs",
"transcript": "ENST00000361715.6",
"protein_id": "ENSP00000355311.2",
"transcript_support_level": 5,
"aa_start": 922,
"aa_end": null,
"aa_length": 979,
"cds_start": 2765,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361715.6"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2765_2768delTTAG",
"hgvs_p": "p.Val922fs",
"transcript": "ENST00000890756.1",
"protein_id": "ENSP00000560815.1",
"transcript_support_level": null,
"aa_start": 922,
"aa_end": null,
"aa_length": 979,
"cds_start": 2765,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890756.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2765_2768delTTAG",
"hgvs_p": "p.Val922fs",
"transcript": "ENST00000968579.1",
"protein_id": "ENSP00000638638.1",
"transcript_support_level": null,
"aa_start": 922,
"aa_end": null,
"aa_length": 979,
"cds_start": 2765,
"cds_end": null,
"cds_length": 2940,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968579.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2762_2765delTTAG",
"hgvs_p": "p.Val921fs",
"transcript": "NM_130834.3",
"protein_id": "NP_570847.2",
"transcript_support_level": null,
"aa_start": 921,
"aa_end": null,
"aa_length": 978,
"cds_start": 2762,
"cds_end": null,
"cds_length": 2937,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130834.3"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2762_2765delTTAG",
"hgvs_p": "p.Val921fs",
"transcript": "ENST00000392437.6",
"protein_id": "ENSP00000376232.2",
"transcript_support_level": 3,
"aa_start": 921,
"aa_end": null,
"aa_length": 978,
"cds_start": 2762,
"cds_end": null,
"cds_length": 2937,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392437.6"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2762_2765delTTAG",
"hgvs_p": "p.Val921fs",
"transcript": "ENST00000890755.1",
"protein_id": "ENSP00000560814.1",
"transcript_support_level": null,
"aa_start": 921,
"aa_end": null,
"aa_length": 978,
"cds_start": 2762,
"cds_end": null,
"cds_length": 2937,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890755.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2753_2756delTTAG",
"hgvs_p": "p.Val918fs",
"transcript": "ENST00000890757.1",
"protein_id": "ENSP00000560816.1",
"transcript_support_level": null,
"aa_start": 918,
"aa_end": null,
"aa_length": 975,
"cds_start": 2753,
"cds_end": null,
"cds_length": 2928,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000890757.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2708_2711delTTAG",
"hgvs_p": "p.Val903fs",
"transcript": "ENST00000392436.7",
"protein_id": "ENSP00000376231.3",
"transcript_support_level": 3,
"aa_start": 903,
"aa_end": null,
"aa_length": 972,
"cds_start": 2708,
"cds_end": null,
"cds_length": 2919,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392436.7"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2732_2735delTTAG",
"hgvs_p": "p.Val911fs",
"transcript": "ENST00000968581.1",
"protein_id": "ENSP00000638640.1",
"transcript_support_level": null,
"aa_start": 911,
"aa_end": null,
"aa_length": 968,
"cds_start": 2732,
"cds_end": null,
"cds_length": 2907,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968581.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2723_2726delTTAG",
"hgvs_p": "p.Val908fs",
"transcript": "ENST00000645553.1",
"protein_id": "ENSP00000494725.1",
"transcript_support_level": null,
"aa_start": 908,
"aa_end": null,
"aa_length": 965,
"cds_start": 2723,
"cds_end": null,
"cds_length": 2898,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000645553.1"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2711_2714delTTAG",
"hgvs_p": "p.Val904fs",
"transcript": "NM_130833.3",
"protein_id": "NP_570846.1",
"transcript_support_level": null,
"aa_start": 904,
"aa_end": null,
"aa_length": 961,
"cds_start": 2711,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_130833.3"
},
{
"aa_ref": "VR",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant",
"splice_region_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OPA1",
"gene_hgnc_id": 8140,
"hgvs_c": "c.2711_2714delTTAG",
"hgvs_p": "p.Val904fs",
"transcript": "ENST00000361150.6",
"protein_id": "ENSP00000354781.2",
"transcript_support_level": 5,
"aa_start": 904,
"aa_end": null,
"aa_length": 961,
"cds_start": 2711,
"cds_end": null,
"cds_length": 2886,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000361150.6"
},
{
"aa_ref": "VR",
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"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
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"alphamissense_score": null,
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"bayesdelnoaf_score": null,
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"phylop100way_score": 9.953,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
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"mitotip_score": null,
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"acmg_score": 22,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS3,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 22,
"benign_score": 0,
"pathogenic_score": 22,
"criteria": [
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"PS3",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_130837.3",
"gene_symbol": "OPA1",
"hgnc_id": 8140,
"effects": [
"frameshift_variant",
"splice_region_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.2873_2876delTTAG",
"hgvs_p": "p.Val958fs"
},
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PS3",
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000822235.1",
"gene_symbol": "ENSG00000306963",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.947_950delAACT",
"hgvs_p": null
},
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PS3",
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "XR_924835.3",
"gene_symbol": "LOC102724808",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.420+1749_420+1752delAACT",
"hgvs_p": null
}
],
"clinvar_disease": " and neuropathy, ataxia, myopathy, normal tension, ophthalmoplegia, susceptibility to,3-Methylglutaconic aciduria type 3,Abortive cerebellar ataxia,Autosomal dominant optic atrophy classic form,Glaucoma,Mitochondrial DNA depletion syndrome 14 (cardioencephalomyopathic type),Mitochondrial disease,OPA1-related disorder,Optic atrophy,Optic atrophy with or without deafness,Retinal dystrophy,See cases,Tip-toe gait,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:23 LP:3 O:2",
"phenotype_combined": "Autosomal dominant optic atrophy classic form|not provided|Abortive cerebellar ataxia|Mitochondrial disease|Optic atrophy with or without deafness, ophthalmoplegia, myopathy, ataxia, and neuropathy|Retinal dystrophy|Glaucoma, normal tension, susceptibility to;Mitochondrial DNA depletion syndrome 14 (cardioencephalomyopathic type);Autosomal dominant optic atrophy classic form;Optic atrophy with or without deafness, ophthalmoplegia, myopathy, ataxia, and neuropathy;Abortive cerebellar ataxia|Tip-toe gait|OPA1-related disorder|See cases|Optic atrophy|3-Methylglutaconic aciduria type 3",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}