MKRN3

makorin ring finger protein 3, the group of Ring finger proteins

Basic information

Region (hg38): 15:23565674-23630075

Previous symbols: [ "ZNF127", "D15S9" ]

Links

ENSG00000179455

∙ NCBI:7681 ∙ OMIM:603856 ∙ HGNC:7114 ∙ Uniprot:Q13064 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

precocious puberty, central, 2 (Strong), mode of inheritance: AD
precocious puberty, central, 2 (Strong), mode of inheritance: AD
precocious puberty, central, 2 (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Central precocious puberty	AD	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; Variants may modify severity of BBS and related disorders due to variants in other BBS-associated genes	Endocrine	23738509
In Precocious puberty, treatment with gonadotropin-releasing hormone receptor analogs/LHRH agonists can be beneficial

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MKRN3 gene.

Inborn_genetic_diseases (59 variants)
not_provided (40 variants)
Precocious_puberty,_central,_2 (11 variants)
MKRN3-related_disorder (8 variants)
Prader-Willi_syndrome (3 variants)
not_specified (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MKRN3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005664.4. 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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				19 clinvar	3 clinvar	22
missense	2 clinvar	1 clinvar	59 clinvar	10 clinvar	1 clinvar	73
nonsense	1 clinvar	1 clinvar	1 clinvar			3
start loss						0
frameshift	4 clinvar	4 clinvar	2 clinvar			10
splice donor/acceptor (+/-2bp)						0
Total	7	6	62	29	4

Highest pathogenic variant AF is 0.0000409028

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MKRN3	protein_coding	protein_coding	ENST00000314520	1	62611

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.278	0.718	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.423	329	308	1.07	0.0000182	3309
Missense in Polyphen		56	73.014	0.76698		867
Synonymous	-2.13	150	120	1.25	0.00000757	1019
Loss of Function	2.45	3	12.2	0.245	6.10e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: E3 ubiquitin ligase catalyzing the covalent attachment of ubiquitin moieties onto substrate proteins. {ECO:0000250, ECO:0000269|PubMed:19066619}.;
Pathway: Prader-Willi and Angelman Syndrome (Consensus)

Recessive Scores

pRec: 0.110

Intolerance Scores

loftool: 0.589
rvis_EVS: -1.13
rvis_percentile_EVS: 6.48

Haploinsufficiency Scores

pHI: 0.0278
hipred: N
hipred_score: 0.158
ghis: 0.479

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.592

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Mkrn3
Phenotype

Gene ontology

Biological process: protein ubiquitination
Cellular component: ribonucleoprotein complex
Molecular function: protein binding;transferase activity;identical protein binding;metal ion binding