MNS1

meiosis specific nuclear structural 1

Basic information

Region (hg38): 15:56421543-56465137

Links

ENSG00000138587 ∙ NCBI:55329 ∙ OMIM:610766 ∙ HGNC:29636 ∙ Uniprot:Q8NEH6 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• heterotaxy, visceral, 9, autosomal, with male infertility (Strong), mode of inheritance: AR
• heterotaxy, visceral, 9, autosomal, with male infertility (Strong), mode of inheritance: AR
• primary ciliary dyskinesia (Disputed Evidence), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Heterotaxy, visceral, 9, autosomal, with male infertility	AR	Cardiovascular	The condition can involve congenital cardiac anomalies, and awareness may allow early identifcation and management	Cardiovascular; Gastrointestinal; Genitourinary	30148830; 31534215

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MNS1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MNS1 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			31	4	1	36
nonsense		3	1			4
start loss						0
frameshift		1				1
inframe indel		1				1
splice donor/acceptor (+/-2bp)						0
splice region			1			1
non coding					1	1
Total	0	5	32	5	2

Variants in MNS1

This is a list of pathogenic ClinVar variants found in the MNS1 region.

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

Position	Type	Phenotype	Significance	ClinVar
15-56427605-G-T		not specified	Uncertain significance (Feb 22, 2023)
15-56427634-T-G		not specified	Uncertain significance (Jun 17, 2024)
15-56427732-G-C		not specified	Uncertain significance (Feb 23, 2023)
15-56428388-A-G		not specified	Uncertain significance (Mar 14, 2023)
15-56428412-T-A		not specified	Uncertain significance (Dec 14, 2023)
15-56429102-C-A		MNS1-related disorder	Benign (Sep 25, 2020)
15-56429168-A-T		not specified	Uncertain significance (Dec 07, 2023)
15-56429175-C-T		not specified	Uncertain significance (Jan 04, 2022)
15-56429184-T-A			Uncertain significance (Oct 30, 2019)
15-56429190-C-T		not specified	Uncertain significance (Oct 03, 2022)
15-56429208-C-T			Benign (Oct 30, 2019)
15-56431377-G-A		Heterotaxy, visceral, 9, autosomal, with male infertility	Uncertain significance (-)
15-56431420-T-G			Likely benign (Oct 01, 2022)
15-56431424-C-A		not specified	Uncertain significance (Feb 28, 2023)
15-56431441-T-C		not specified	Uncertain significance (Oct 05, 2023)
15-56431444-C-G		not specified	Uncertain significance (Jan 25, 2023)
15-56431462-G-A		not specified	Uncertain significance (May 05, 2022)
15-56431467-T-C		not specified	Uncertain significance (Dec 21, 2022)
15-56431494-C-T		MNS1-related disorder	Likely benign (Feb 20, 2023)
15-56434161-G-A		not specified	Uncertain significance (Apr 20, 2024)
15-56434203-G-T		not specified	Uncertain significance (Jun 22, 2021)
15-56434244-C-T		Heterotaxy, visceral, 9, autosomal, with male infertility	Uncertain significance (Jun 06, 2023)
15-56434245-G-C		not specified	Uncertain significance (Oct 14, 2023)
15-56434247-T-A		not specified	Uncertain significance (Jan 24, 2023)
15-56434293-C-T		not specified	Uncertain significance (Jun 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MNS1	protein_coding	protein_coding	ENST00000260453	10	43594

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.10e-21	0.00167	125562	0	174	125736	0.000692

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.439	270	250	1.08	0.0000130	3351
Missense in Polyphen		85	75.248	1.1296		1078
Synonymous	-0.554	84	77.8	1.08	0.00000363	742
Loss of Function	0.0721	32	32.4	0.986	0.00000171	394

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000922	0.000918
Ashkenazi Jewish	0.000105	0.0000992
East Asian	0.000899	0.000870
Finnish	0.0000978	0.0000924
European (Non-Finnish)	0.000669	0.000660
Middle Eastern	0.000899	0.000870
South Asian	0.00190	0.00180
Other	0.000494	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the control of meiotic division and germ cell differentiation through regulation of pairing and recombination during meiosis. {ECO:0000250}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• rvis_EVS: 0.13
• rvis_percentile_EVS: 63.49

Haploinsufficiency Scores

• pHI: 0.103
• hipred: N
• hipred_score: 0.244
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.642

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mns1
• Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; cellular phenotype; respiratory system phenotype; reproductive system 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)

Zebrafish Information Network

• Gene name: mns1
• Affected structure: otolith
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: spermatogenesis;cilium organization;positive regulation of cilium assembly;meiotic cell cycle;left/right axis specification
• Cellular component: nuclear envelope;intermediate filament;axoneme;motile cilium;sperm flagellum
• Molecular function: identical protein binding