MYORG

myogenesis regulating glycosidase (putative), the group of Glycoside hydrolase family 31

Basic information

Region (hg38): 9:34366666-34376898

Previous symbols: [ "KIAA1161" ]

Links

ENSG00000164976 ∙ NCBI:57462 ∙ OMIM:618255 ∙ HGNC:19918 ∙ Uniprot:Q6NSJ0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• basal ganglia calcification, idiopathic, 7, autosomal recessive (Strong), mode of inheritance: AR
• basal ganglia calcification, idiopathic, 7, autosomal recessive (Strong), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 7, autosomal recessive (Strong), mode of inheritance: AR
• bilateral striopallidodentate calcinosis (Supportive), mode of inheritance: AD
• basal ganglia calcification, idiopathic, 7, autosomal recessive (Definitive), mode of inheritance: AR
• basal ganglia calcification, idiopathic, 7, autosomal recessive (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Basal ganglia calcification, idiopathic, 7, autosomal recessive	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Neurologic	29910000; 30460687; 30656188; 30649222

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYORG gene.

• not provided (4 variants)
• Basal ganglia calcification, idiopathic, 7, autosomal recessive (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYORG gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			1	39	4	44
missense		3	127	2	5	137
nonsense	3	8			1	12
start loss						0
frameshift	2	6	2	1		11
inframe indel		1	6			7
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	5	18	136	42	13

Variants in MYORG

This is a list of pathogenic ClinVar variants found in the MYORG region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
9-34370703-TG-T			Benign (May 12, 2021)
9-34370807-C-A		not specified	Uncertain significance (Dec 01, 2022)
9-34370822-C-A		not specified	Uncertain significance (Jan 19, 2022)
9-34370823-G-T			Likely benign (Aug 15, 2022)
9-34370841-C-T			Likely benign (Feb 24, 2024)
9-34370861-C-G			Uncertain significance (Dec 01, 2020)
9-34370903-T-C			Uncertain significance (Aug 09, 2024)
9-34370908-G-A		not specified	Uncertain significance (Jun 13, 2023)
9-34370909-C-A		not specified	Uncertain significance (Jun 13, 2023)
9-34370910-G-C			Likely benign (Jul 01, 2023)
9-34370911-G-A		not specified	Uncertain significance (Jan 31, 2022)
9-34370913-C-G		not specified	Uncertain significance (Mar 01, 2024)
9-34370913-C-T			Likely benign (Dec 03, 2021)
9-34370920-ACGTCG-A			Likely pathogenic (Apr 01, 2024)
9-34370924-C-T			Uncertain significance (Sep 21, 2019)
9-34370925-G-C			Likely benign (Dec 12, 2023)
9-34370938-C-G		not specified	Uncertain significance (Aug 12, 2024)
9-34370953-G-A		Basal ganglia calcification, idiopathic, 7, autosomal recessive	Uncertain significance (Sep 01, 2022)
9-34370965-A-G			Uncertain significance (Feb 11, 2022)
9-34370965-A-T		Basal ganglia calcification, idiopathic, 7, autosomal recessive	Uncertain significance (Jun 13, 2019)
9-34370967-C-G			Likely benign (Jan 08, 2024)
9-34370972-C-T			Uncertain significance (Aug 24, 2023)
9-34370977-A-G		Basal ganglia calcification, idiopathic, 7, autosomal recessive • Inborn genetic diseases	Conflicting classifications of pathogenicity (Oct 13, 2023)
9-34370977-A-T			Uncertain significance (Oct 29, 2024)
9-34371004-G-A		not specified	Uncertain significance (May 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYORG	protein_coding	protein_coding	ENST00000297625	1	10184

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.09e-11	0.0879	124930	0	44	124974	0.000176

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.39	436	526	0.829	0.0000427	4294
Missense in Polyphen		213	245.13	0.86893		2150
Synonymous	0.0280	248	249	0.998	0.0000220	1442
Loss of Function	0.399	18	19.9	0.904	0.00000103	191

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000449	0.000431
Ashkenazi Jewish	0.0000999	0.0000993
East Asian	0.000224	0.000223
Finnish	0.00	0.00
European (Non-Finnish)	0.000275	0.000265
Middle Eastern	0.000224	0.000223
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Putative glycosidase. Promotes myogenesis by activating AKT signaling through the maturation and secretion of IGF2. {ECO:0000250|UniProtKB:Q69ZQ1}.
• Pathway: Ectoderm Differentiation (Consensus)

Haploinsufficiency Scores

• pHI: 0.226
• hipred: N
• hipred_score: 0.379
• ghis: 0.535

Mouse Genome Informatics

• Gene name: AI464131
• Phenotype: cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan)

Gene ontology

• Biological process: carbohydrate metabolic process;glycoside catabolic process;positive regulation of insulin-like growth factor receptor signaling pathway;skeletal muscle fiber development;positive regulation of protein kinase B signaling
• Cellular component: endoplasmic reticulum membrane;integral component of membrane;nuclear membrane
• Molecular function: hydrolase activity, hydrolyzing O-glycosyl compounds