MYEF2

myelin expression factor 2, the group of RNA binding motif containing

Basic information

Region (hg38): 15:48134631-48178353

Links

ENSG00000104177 ∙ NCBI:50804 ∙ OMIM:619395 ∙ HGNC:17940 ∙ Uniprot:Q9P2K5 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MYEF2 gene.

• not provided (114 variants)
• Inborn genetic diseases (27 variants)
• Oculocutaneous albinism type 6 (4 variants)
• not specified (3 variants)
• Oculocutaneous albinism (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYEF2 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						0
missense			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding	11	6	67	30	1	115
Total	11	6	86	31	1

Highest pathogenic variant AF is 0.0000461

Variants in MYEF2

This is a list of pathogenic ClinVar variants found in the MYEF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-48134876-T-C			Uncertain significance (Jan 16, 2022)
15-48134886-CT-C			Pathogenic (Nov 07, 2018)
15-48134888-C-G		Oculocutaneous albinism type 6	Pathogenic (Mar 01, 2023)
15-48134891-C-T			Uncertain significance (Oct 17, 2022)
15-48134892-A-C			Likely benign (Jan 15, 2024)
15-48134896-T-A			Uncertain significance (Oct 07, 2021)
15-48134897-C-G		Skin/hair/eye pigmentation, variation in, 4	Pathogenic (Mar 26, 2019)
15-48134897-C-T			Uncertain significance (Oct 24, 2022)
15-48134899-T-C			Uncertain significance (Feb 11, 2022)
15-48134907-C-T			Likely benign (Jul 29, 2022)
15-48134912-TCAGAGACTGTG-T			Pathogenic (Feb 02, 2022)
15-48134915-G-A		Oculocutaneous albinism type 6	Pathogenic (Sep 21, 2022)
15-48134922-T-A		Oculocutaneous albinism type 6	Pathogenic (Jan 17, 2017)
15-48134927-C-T			Uncertain significance (Nov 01, 2022)
15-48134928-G-A		SLC24A5-related disorder	Conflicting classifications of pathogenicity (Jul 03, 2023)
15-48134928-G-C			Likely benign (Sep 01, 2022)
15-48134931-C-T			Likely benign (Nov 15, 2022)
15-48134938-A-G			Uncertain significance (Jun 28, 2022)
15-48134940-T-A			Conflicting classifications of pathogenicity (Jan 01, 2024)
15-48134952-T-C			Likely benign (Nov 20, 2023)
15-48134954-T-C			Uncertain significance (Mar 18, 2022)
15-48134956-G-C		Inborn genetic diseases	Uncertain significance (Oct 20, 2023)
15-48134957-GTATAA-G			Pathogenic (Jun 05, 2022)
15-48134963-T-TATTA		Skin/hair/eye pigmentation, variation in, 4	association (Dec 15, 2012)
15-48134977-G-A			Uncertain significance (Nov 28, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYEF2	protein_coding	protein_coding	ENST00000324324	17	39090

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.635	0.365	125086	4	655	125745	0.00262

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.53	258	337	0.766	0.0000173	3962
Missense in Polyphen		75	125.2	0.59903		1480
Synonymous	2.97	66	105	0.631	0.00000539	1091
Loss of Function	4.28	7	33.9	0.207	0.00000185	414

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00292	0.00292
Ashkenazi Jewish	0.00229	0.00228
East Asian	0.0000598	0.0000544
Finnish	0.000231	0.000231
European (Non-Finnish)	0.00439	0.00435
Middle Eastern	0.0000598	0.0000544
South Asian	0.000954	0.000948
Other	0.00395	0.00375

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Transcriptional repressor of the myelin basic protein gene (MBP). Binds to the proximal MB1 element 5'-TTGTCC-3' of the MBP promoter. Its binding to MB1 and function are inhibited by PURA (By similarity). {ECO:0000250}.
• Pathway: Physiological and Pathological Hypertrophy of the Heart;MicroRNAs in cardiomyocyte hypertrophy;TFs Regulate miRNAs related to cardiac hypertrophy;Mitochondrial Gene Expression (Consensus)

Recessive Scores

• pRec: 0.308

Intolerance Scores

• loftool: 0.531
• rvis_EVS: -0.07
• rvis_percentile_EVS: 48.54

Haploinsufficiency Scores

• pHI: 0.385
• hipred: Y
• hipred_score: 0.735
• ghis: 0.531

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.826

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Myef2

Zebrafish Information Network

• Gene name: myef2
• Affected structure: hematopoietic stem cell
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;myotube differentiation;neuron differentiation;regulation of mRNA stability involved in response to oxidative stress
• Cellular component: nucleus;cytoplasm;post-mRNA release spliceosomal complex;ribonucleoprotein complex
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;single-stranded DNA binding;RNA binding;mRNA binding