KY

kyphoscoliosis peptidase

Basic information

Region (hg38): 3:134599923-134651636

Links

ENSG00000174611NCBI:339855OMIM:605739HGNC:26576Uniprot:Q8NBH2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Myopathy, myofibrillar, 7ARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingMusculoskeletal27484770; 27485408

ClinVar

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

  • Inborn_genetic_diseases (66 variants)
  • not_provided (56 variants)
  • Myofibrillar_myopathy_7 (22 variants)
  • KY-related_disorder (15 variants)
  • Hereditary_spastic_paraplegia (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. These statistics are base on transcript: NM_000178554.6. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
13
clinvar
3
clinvar
17
missense
1
clinvar
75
clinvar
9
clinvar
1
clinvar
86
nonsense
3
clinvar
3
clinvar
6
start loss
0
frameshift
2
clinvar
2
clinvar
4
splice donor/acceptor (+/-2bp)
1
clinvar
1
Total 5 3 80 22 4

Highest pathogenic variant AF is 0.00000208018

Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
KYprotein_codingprotein_codingENST00000423778 1148499
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.54e-100.9451246400641247040.000257
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.8263313760.8800.00002024360
Missense in Polyphen80117.70.679691404
Synonymous1.031401560.8950.000008891238
Loss of Function2.052133.90.6200.00000176359

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0005430.000529
Ashkenazi Jewish0.000.00
East Asian0.0004550.000445
Finnish0.000.00
European (Non-Finnish)0.0002680.000257
Middle Eastern0.0004550.000445
South Asian0.0003980.000392
Other0.0003310.000330

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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