MND1

meiotic nuclear divisions 1

Basic information

Region (hg38): 4:153344649-153415118

Links

ENSG00000121211 ∙ NCBI:84057 ∙ OMIM:611422 ∙ HGNC:24839 ∙ Uniprot:Q9BWT6 ∙ 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 MND1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MND1 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					1	1
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	13	0	1

Variants in MND1

This is a list of pathogenic ClinVar variants found in the MND1 region.

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

Position	Type	Phenotype	Significance	ClinVar
4-153350059-T-G			Benign (Dec 31, 2019)
4-153355660-G-A		not specified	Uncertain significance (Oct 03, 2023)
4-153355675-G-T		not specified	Uncertain significance (Feb 21, 2024)
4-153358479-A-G		not specified	Uncertain significance (Oct 14, 2023)
4-153358525-T-C		not specified	Uncertain significance (Jun 21, 2021)
4-153358575-A-G		not specified	Uncertain significance (Sep 16, 2021)
4-153358584-C-T		not specified	Uncertain significance (Nov 02, 2023)
4-153358597-A-G		not specified	Likely benign (Mar 30, 2024)
4-153358621-A-G		not specified	Uncertain significance (May 12, 2024)
4-153394305-T-C		not specified	Uncertain significance (Jul 13, 2021)
4-153394326-G-T		not specified	Uncertain significance (Dec 02, 2021)
4-153394335-C-T		not specified	Uncertain significance (Jun 06, 2023)
4-153397259-G-A		not specified	Uncertain significance (Mar 31, 2023)
4-153397281-G-C		not specified	Uncertain significance (Jan 09, 2024)
4-153409011-G-C		not specified	Uncertain significance (May 03, 2023)
4-153414812-T-C			Benign (Dec 31, 2019)
4-153414852-G-A		not specified	Uncertain significance (Mar 23, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MND1	protein_coding	protein_coding	ENST00000240488	8	70470

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.28e-9	0.177	125699	0	47	125746	0.000187

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.412	89	101	0.884	0.00000501	1352
Missense in Polyphen		22	28.051	0.78428		418
Synonymous	1.44	20	30.1	0.665	0.00000149	335
Loss of Function	0.393	14	15.7	0.893	9.70e-7	181

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000836	0.000834
Ashkenazi Jewish	0.00	0.00
East Asian	0.000219	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.000154	0.000149
Middle Eastern	0.000219	0.000217
South Asian	0.000135	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for proper homologous chromosome pairing and efficient cross-over and intragenic recombination during meiosis (By similarity). Stimulates both DMC1- and RAD51-mediated homologous strand assimilation, which is required for the resolution of meiotic double-strand breaks. {ECO:0000250|UniProtKB:Q8K396, ECO:0000269|PubMed:16407260}.

Recessive Scores

• pRec: 0.111

Intolerance Scores

• loftool: 0.527
• rvis_EVS: -0.25
• rvis_percentile_EVS: 35.42

Haploinsufficiency Scores

• pHI: 0.564
• hipred: Y
• hipred_score: 0.635
• ghis: 0.714

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: H
• gene_indispensability_pred: N
• gene_indispensability_score: 0.476

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mnd1
• Phenotype: homeostasis/metabolism phenotype; cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: reciprocal meiotic recombination
• Cellular component: nucleus
• Molecular function: double-stranded DNA binding