MEIG1

meiosis/spermiogenesis associated 1

Basic information

Region (hg38): 10:14959388-14988050

Links

ENSG00000197889 ∙ NCBI:644890 ∙ OMIM:614174 ∙ HGNC:23429 ∙ Uniprot:Q5JSS6 ∙ 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 MEIG1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MEIG1 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			9			9
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	9	0	0

Variants in MEIG1

This is a list of pathogenic ClinVar variants found in the MEIG1 region.

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

Position	Type	Phenotype	Significance	ClinVar
10-14966476-G-A		not specified	Uncertain significance (Jul 09, 2021)
10-14966497-C-T		not specified	Uncertain significance (Jun 21, 2023)
10-14966503-G-A		not specified	Uncertain significance (Aug 02, 2021)
10-14966512-A-G		not specified	Uncertain significance (May 01, 2022)
10-14966513-A-C		not specified	Uncertain significance (Aug 10, 2021)
10-14966515-A-T		not specified	Uncertain significance (Jul 31, 2024)
10-14966565-C-T		not specified	Uncertain significance (Feb 15, 2023)
10-14966577-G-A		not specified	Uncertain significance (Sep 14, 2021)
10-14966592-A-C		not specified	Uncertain significance (Mar 16, 2022)
10-14972519-C-T		not specified	Uncertain significance (Aug 08, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MEIG1	protein_coding	protein_coding	ENST00000407572	2	28612

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000327	0.380	125724	0	11	125735	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.225	53	48.6	1.09	0.00000269	577
Missense in Polyphen		18	16.177	1.1127		200
Synonymous	0.113	15	15.6	0.964	8.48e-7	140
Loss of Function	-0.117	5	4.72	1.06	1.99e-7	59

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000586	0.0000586
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000792	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for spermiogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.0955

Intolerance Scores

• loftool: 0.636
• rvis_EVS: 0.35
• rvis_percentile_EVS: 73.97

Haploinsufficiency Scores

• pHI: 0.140
• hipred: N
• hipred_score: 0.354

Essentials

• essential_gene_CRISPR: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.510

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Meig1
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: spermatogenesis;cell differentiation
• Cellular component: nucleus