MYDGF

myeloid derived growth factor

Basic information

Region (hg38): 19:4641373-4670362

Previous symbols: [ "IL27", "IL27w", "C19orf10" ]

Links

ENSG00000074842 ∙ NCBI:56005 ∙ OMIM:606746 ∙ HGNC:16948 ∙ Uniprot:Q969H8 ∙ 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 MYDGF gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MYDGF 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			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	13	0	0

Variants in MYDGF

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

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

Position	Type	Phenotype	Significance	ClinVar
19-4652026-C-T		not specified	Uncertain significance (Sep 01, 2021)
19-4652110-G-A		not specified	Uncertain significance (Dec 07, 2023)
19-4652141-G-A		not specified	Uncertain significance (Apr 15, 2024)
19-4652203-G-C		not specified	Uncertain significance (Sep 17, 2021)
19-4652224-G-A		not specified	Uncertain significance (Dec 18, 2023)
19-4652311-G-T		not specified	Uncertain significance (May 15, 2024)
19-4652405-G-A		not specified	Uncertain significance (Dec 15, 2023)
19-4658019-G-A		not specified	Uncertain significance (Jul 26, 2022)
19-4658021-G-A		not specified	Uncertain significance (Feb 28, 2024)
19-4658069-C-T		not specified	Uncertain significance (Dec 28, 2022)
19-4659939-T-C		not specified	Uncertain significance (Jan 18, 2022)
19-4659991-A-T		not specified	Uncertain significance (Sep 14, 2022)
19-4660680-C-T		not specified	Uncertain significance (Dec 14, 2021)
19-4660701-G-A		not specified	Uncertain significance (Jun 03, 2024)
19-4664907-C-T		not specified	Uncertain significance (Dec 14, 2023)
19-4670219-G-T		not specified	Uncertain significance (Jul 14, 2021)
19-4670220-C-A		not specified	Uncertain significance (Jan 23, 2023)
19-4670243-G-A		not specified	Uncertain significance (Mar 25, 2024)
19-4670250-C-T		not specified	Uncertain significance (Oct 13, 2023)
19-4670295-T-A		not specified	Uncertain significance (Sep 15, 2021)
19-4670315-C-A		not specified	Uncertain significance (Sep 12, 2023)
19-4670315-C-T		not specified	Uncertain significance (Jun 16, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MYDGF	protein_coding	protein_coding	ENST00000262947	6	28997

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000349	0.365	125723	0	22	125745	0.0000875

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.857	71	94.4	0.752	0.00000513	1090
Missense in Polyphen		30	33.499	0.89556		386
Synonymous	-0.769	48	41.7	1.15	0.00000260	333
Loss of Function	0.385	9	10.3	0.871	5.40e-7	107

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000212	0.000212
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000618	0.0000615
Middle Eastern	0.0000544	0.0000544
South Asian	0.000163	0.000163
Other	0.000659	0.000652

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Bone marrow-derived monocyte and paracrine-acting protein that promotes cardiac myocyte survival and adaptive angiogenesis for cardiac protection and/or repair after myocardial infarction (MI). Stimulates endothelial cell proliferation through a MAPK1/3-, STAT3- and CCND1-mediated signaling pathway. Inhibits cardiac myocyte apoptosis in a PI3K/AKT-dependent signaling pathway (By similarity). Involved in endothelial cell proliferation and angiogenesis (PubMed:25581518). {ECO:0000250|UniProtKB:Q9CPT4, ECO:0000269|PubMed:25581518}.
• Pathway: XBP1(S) activates chaperone genes (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• rvis_EVS: 0.22
• rvis_percentile_EVS: 67.92

Haploinsufficiency Scores

• pHI: 0.0846
• hipred: N
• hipred_score: 0.370
• ghis: 0.484

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Mydgf
• Phenotype: immune system 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); homeostasis/metabolism phenotype

Gene ontology

• Biological process: angiogenesis;positive regulation of protein phosphorylation;positive regulation of endothelial cell proliferation;apoptotic process;positive regulation of phosphatidylinositol 3-kinase signaling;IRE1-mediated unfolded protein response;negative regulation of apoptotic process;positive regulation of MAPK cascade;positive regulation of angiogenesis;positive regulation of transcription by RNA polymerase II;positive regulation of protein kinase B signaling
• Cellular component: extracellular space;endoplasmic reticulum lumen;endoplasmic reticulum-Golgi intermediate compartment
• Molecular function: protein binding