KY

kyphoscoliosis peptidase

Basic information

Region (hg38): 3:134599923-134651636

Links

ENSG00000174611 ∙ NCBI:339855 ∙ OMIM:605739 ∙ HGNC:26576 ∙ Uniprot:Q8NBH2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• kyphosis-lateral tongue atrophy-myofibrillar myopathy syndrome (Supportive), mode of inheritance: AR
• kyphoscoliosis-lateral tongue atrophy-hereditary spastic paraplegia syndrome (Supportive), mode of inheritance: AR
• myofibrillar myopathy 7 (Moderate), mode of inheritance: AR
• myofibrillar myopathy 7 (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Myopathy, myofibrillar, 7	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	Musculoskeletal	27484770; 27485408

ClinVar

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

• Myofibrillar myopathy 7 (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the KY 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				13	7	20
missense			38	3	1	42
nonsense	1		1			2
start loss						0
frameshift		1				1
inframe indel						0
splice donor/acceptor (+/-2bp)			1			1
splice region			1	4		5
non coding				16	14	30
Total	1	1	40	32	22

Variants in KY

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

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

Position	Type	Phenotype	Significance	ClinVar
3-134603271-G-A			Benign (Mar 06, 2021)
3-134603321-C-A			Benign (Mar 06, 2021)
3-134603375-C-G			Likely benign (May 13, 2021)
3-134603664-C-A		Myofibrillar myopathy 7 • Inborn genetic diseases	Uncertain significance (Oct 19, 2024)
3-134603670-G-C		Myofibrillar myopathy 7	Uncertain significance (Mar 30, 2023)
3-134603672-T-C			Benign (Mar 29, 2021)
3-134603676-C-T		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jul 30, 2024)
3-134603787-C-T		Inborn genetic diseases	Uncertain significance (Dec 19, 2022)
3-134603788-G-A			Benign (Dec 31, 2019)
3-134603792-G-A		KY-related disorder	Likely benign (May 31, 2019)
3-134603831-G-T		Inborn genetic diseases	Uncertain significance (Jun 13, 2023)
3-134603839-C-T		Inborn genetic diseases	Uncertain significance (May 25, 2022)
3-134603847-C-A			Uncertain significance (Aug 01, 2024)
3-134603900-A-G		Myofibrillar myopathy 7	Benign (Aug 19, 2021)
3-134603913-A-G		Inborn genetic diseases	Uncertain significance (Sep 17, 2021)
3-134603950-C-T		Inborn genetic diseases	Uncertain significance (Jun 22, 2021)
3-134603969-C-T		KY-related disorder	Benign (Dec 31, 2019)
3-134603972-G-C		Myofibrillar myopathy 7	Benign (Aug 19, 2021)
3-134604001-C-T		KY-related disorder	Likely benign (Sep 08, 2018)
3-134604002-G-A			Benign/Likely benign (Oct 17, 2021)
3-134604015-C-T		Inborn genetic diseases	Uncertain significance (Apr 15, 2024)
3-134604033-T-C		Inborn genetic diseases	Uncertain significance (Nov 28, 2024)
3-134604035-G-A			Likely benign (Apr 02, 2021)
3-134604036-C-T		Inborn genetic diseases	Uncertain significance (Jul 30, 2024)
3-134604039-C-T			Uncertain significance (May 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
KY	protein_coding	protein_coding	ENST00000423778	11	48499

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.54e-10	0.945	124640	0	64	124704	0.000257

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.826	331	376	0.880	0.0000202	4360
Missense in Polyphen		80	117.7	0.67969		1404
Synonymous	1.03	140	156	0.895	0.00000889	1238
Loss of Function	2.05	21	33.9	0.620	0.00000176	359

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000543	0.000529
Ashkenazi Jewish	0.00	0.00
East Asian	0.000455	0.000445
Finnish	0.00	0.00
European (Non-Finnish)	0.000268	0.000257
Middle Eastern	0.000455	0.000445
South Asian	0.000398	0.000392
Other	0.000331	0.000330

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable cytoskeleton-associated protease required for normal muscle growth. Involved in function, maturation and stabilization of the neuromuscular junction. May act by cleaving muscle-specific proteins such as FLNC (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.150

Intolerance Scores

• loftool: 0.493
• rvis_EVS: -1.2
• rvis_percentile_EVS: 5.83

Haploinsufficiency Scores

• pHI: 0.399
• hipred: N
• hipred_score: 0.170
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.223

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Ky
• Phenotype: muscle phenotype; growth/size/body region phenotype; reproductive system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); skeleton phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype

Gene ontology

• Biological process: proteolysis
• Cellular component: cytoskeleton;Z disc
• Molecular function: peptidase activity