MSGN1

mesogenin 1

Basic information

Region (hg38): 2:17816460-17817798

Links

ENSG00000151379 ∙ NCBI:343930 ∙ OMIM:612209 ∙ HGNC:14907 ∙ Uniprot:A6NI15 ∙ 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 MSGN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MSGN1 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			14	1		15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	1	0

Variants in MSGN1

This is a list of pathogenic ClinVar variants found in the MSGN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-17816529-T-G		not specified	Uncertain significance (Apr 11, 2023)
2-17816536-G-C		not specified	Uncertain significance (Jul 21, 2022)
2-17816546-A-G		not specified	Likely benign (Nov 07, 2023)
2-17816600-G-T		not specified	Uncertain significance (May 05, 2023)
2-17816638-G-C		not specified	Uncertain significance (Apr 22, 2022)
2-17816655-G-A		not specified	Uncertain significance (Mar 13, 2023)
2-17816685-A-C		not specified	Uncertain significance (Dec 03, 2021)
2-17816771-G-A		not specified	Uncertain significance (Jan 05, 2022)
2-17816805-A-G		not specified	Uncertain significance (Jun 07, 2024)
2-17816823-C-A		not specified	Uncertain significance (Apr 01, 2024)
2-17816838-G-A		not specified	Uncertain significance (May 03, 2023)
2-17816870-A-G		not specified	Uncertain significance (Sep 22, 2022)
2-17816978-G-A		not specified	Uncertain significance (Jan 09, 2024)
2-17816993-G-A		not specified	Uncertain significance (Jan 04, 2022)
2-17817068-C-T		not specified	Uncertain significance (Dec 22, 2023)
2-17817069-G-A		not specified	Uncertain significance (Jul 20, 2021)
2-17817095-G-A		not specified	Uncertain significance (Sep 25, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MSGN1	protein_coding	protein_coding	ENST00000281047	1	606

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0720	0.755	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.601	99	117	0.844	0.00000691	1243
Missense in Polyphen		25	34.887	0.71661		396
Synonymous	-0.260	55	52.6	1.05	0.00000327	416
Loss of Function	0.956	2	4.08	0.490	1.73e-7	49

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: Involved in specifying the paraxial, but not dorsal, mesoderm. May regulate the expression of T-box transcription factors required for mesoderm formation and differentiation (By similarity). {ECO:0000250}.
• Pathway: Mesodermal Commitment Pathway (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.221
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.56

Haploinsufficiency Scores

• pHI: 0.275
• hipred: N
• hipred_score: 0.187

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.119

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Msgn1
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); 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); limbs/digits/tail phenotype; skeleton phenotype; growth/size/body region phenotype; muscle phenotype

Zebrafish Information Network

• Gene name: msgn1
• Affected structure: post-vent region
• Phenotype tag: abnormal
• Phenotype quality: has extra parts of type

Gene ontology

• Biological process: mesoderm formation;somitogenesis;segment specification;cell differentiation;positive regulation of transcription by RNA polymerase II
• Cellular component: nucleus
• Molecular function: RNA polymerase II proximal promoter sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;chromatin binding;protein dimerization activity