EMG1

EMG1 N1-specific pseudouridine methyltransferase, the group of SPOUT methyltransferase domain containing|SSU processome

Basic information

Region (hg38): 12:6970912-6979936

Links

ENSG00000126749 ∙ NCBI:10436 ∙ OMIM:611531 ∙ HGNC:16912 ∙ Uniprot:Q92979 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Bowen-Conradi syndrome (Strong), mode of inheritance: AR
• Bowen-Conradi syndrome (Moderate), mode of inheritance: AR
• Bowen-Conradi syndrome (Supportive), mode of inheritance: AR
• Bowen-Conradi syndrome (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bowen-Conradi syndrome	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	Craniofacial; Musculoskeletal; Neurologic	974244; 484596; 12838567; 15578624; 19463982

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the EMG1 gene.

• Inborn genetic diseases (13 variants)
• not provided (10 variants)
• not specified (1 variants)
• Bowen-Conradi syndrome (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the EMG1 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				3	4	7
missense			3	1	1	5
nonsense						0
start loss						0
frameshift					1	1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding			10			10
Total	0	0	13	4	6

Variants in EMG1

This is a list of pathogenic ClinVar variants found in the EMG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-6970938-T-C			Benign (Dec 31, 2019)
12-6970961-G-T			Benign/Likely benign (Dec 31, 2019)
12-6970965-C-G		EMG1-related disorder	Likely benign (Sep 17, 2019)
12-6971024-C-G		not specified	Benign (Feb 13, 2015)
12-6971047-A-AG		Bowen-Conradi syndrome	Benign (Jul 30, 2021)
12-6971049-G-G			Likely benign (-)
12-6974359-A-C			Benign (Mar 03, 2015)
12-6974419-G-A			Likely benign (Dec 31, 2019)
12-6974427-A-G		Bowen-Conradi syndrome	Pathogenic (Jun 01, 2009)
12-6974428-T-C			Likely benign (Dec 31, 2019)
12-6975083-C-T			Likely benign (Sep 21, 2017)
12-6975093-A-G		Inborn genetic diseases	Uncertain significance (Nov 22, 2022)
12-6975270-T-C			Benign (Dec 31, 2019)
12-6975297-C-T		EMG1-related disorder	Likely benign (Jul 03, 2020)
12-6975298-C-T		Inborn genetic diseases	Uncertain significance (Aug 14, 2023)
12-6975333-C-T			Benign (Dec 31, 2019)
12-6975742-C-G		Inborn genetic diseases	Uncertain significance (Mar 16, 2022)
12-6975776-C-G			Likely benign (Dec 31, 2019)
12-6975817-A-C		EMG1-related disorder	Likely benign (May 05, 2020)
12-6977155-C-G		not specified	Uncertain significance (Sep 16, 2021)
12-6977208-T-C		not specified	Uncertain significance (Feb 08, 2023)
12-6977229-A-T		not specified	Uncertain significance (Nov 08, 2022)
12-6977231-A-G		not specified	Uncertain significance (Sep 29, 2023)
12-6977497-G-A		not specified	Uncertain significance (Oct 27, 2022)
12-6977725-T-C		not specified	Uncertain significance (Jun 08, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
EMG1	protein_coding	protein_coding	ENST00000261406	7	33113

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000147	0.658	124615	0	22	124637	0.0000883

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.304	147	137	1.07	0.00000699	1565
Missense in Polyphen
Synonymous	-1.56	64	49.9	1.28	0.00000232	488
Loss of Function	0.938	9	12.6	0.715	7.84e-7	125

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000261	0.000258
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000167
Finnish	0.000139	0.000139
European (Non-Finnish)	0.0000718	0.0000708
Middle Eastern	0.000167	0.000167
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP