M1AP

meiosis 1 associated protein

Basic information

Region (hg38): 2:74557883-74648338

Previous symbols: [ "C2orf65" ]

Links

ENSG00000159374 ∙ NCBI:130951 ∙ OMIM:619098 ∙ HGNC:25183 ∙ Uniprot:Q8TC57 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• spermatogenic failure 48 (Limited), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Spermatogenic failure 48	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	Genitourinary	32017041; 32673564

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the M1AP gene.

• Spermatogenic failure 48 (1 variants)
• Spermatogenesis maturation arrest (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the M1AP 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	2		3
missense		1	33	1		35
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)	1					1
splice region			1			1
non coding						0
Total	1	1	34	3	0

Variants in M1AP

This is a list of pathogenic ClinVar variants found in the M1AP region.

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

Position	Type	Phenotype	Significance	ClinVar
2-74558875-C-T		Spermatogenesis maturation arrest • Spermatogenic failure 48	Pathogenic (Feb 04, 2020)
2-74560146-G-A			Benign (Nov 01, 2024)
2-74560158-G-A		not specified	Likely benign (Oct 29, 2021)
2-74560159-G-A		not specified	Uncertain significance (Jan 26, 2022)
2-74560164-C-T		not specified	Uncertain significance (Oct 26, 2021)
2-74560267-C-G		not specified	Uncertain significance (Jul 14, 2023)
2-74560284-A-G		Non-obstructive azoospermia	Uncertain significance (May 11, 2020)
2-74562222-C-T		not specified	Uncertain significance (May 27, 2022)
2-74562265-G-A			Likely benign (Apr 01, 2024)
2-74562284-A-G		not specified	Uncertain significance (May 23, 2024)
2-74562293-G-A		not specified	Uncertain significance (Oct 12, 2022)
2-74562332-G-A		Non-obstructive azoospermia • Spermatogenic failure 48	Uncertain significance (May 11, 2020)
2-74575427-TGGGTACTCACCA-T		Male infertility	Pathogenic (Feb 15, 2024)
2-74575541-T-C		not specified	Uncertain significance (Jan 10, 2023)
2-74575563-C-T		Non-obstructive azoospermia • Spermatogenic failure 48	Uncertain significance (May 11, 2020)
2-74576527-T-C			Uncertain significance (Oct 01, 2023)
2-74576546-A-C		not specified	Uncertain significance (Oct 30, 2023)
2-74576549-G-A		not specified	Uncertain significance (Sep 17, 2021)
2-74576591-C-T		Spermatogenic failure 48 • Cryptozoospermia • Non-obstructive azoospermia	Uncertain significance (Aug 23, 2021)
2-74576615-C-T		not specified	Uncertain significance (Feb 05, 2024)
2-74576617-C-T		not specified	Uncertain significance (Mar 07, 2024)
2-74581766-C-CA		Non-obstructive azoospermia • Spermatogenic failure 48 • Male infertility with azoospermia or oligozoospermia due to single gene mutation	Conflicting classifications of pathogenicity (Dec 18, 2023)
2-74581794-C-T		not specified	Uncertain significance (Oct 01, 2024)
2-74581841-G-C		not specified	Uncertain significance (Dec 18, 2023)
2-74607052-T-C		Spermatogenic failure 48	Uncertain significance (Nov 09, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
M1AP	protein_coding	protein_coding	ENST00000290536	10	90456

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.16e-19	0.00232	125621	0	127	125748	0.000505

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.613	265	295	0.900	0.0000151	3461
Missense in Polyphen		93	103.35	0.89988		1220
Synonymous	-0.284	123	119	1.03	0.00000650	1067
Loss of Function	-0.119	28	27.3	1.02	0.00000153	286

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00183	0.00183
Ashkenazi Jewish	0.00	0.00
East Asian	0.000164	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000344	0.000343
Middle Eastern	0.000164	0.000163
South Asian	0.00160	0.00157
Other	0.000326	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for meiosis I progression during spermatogenesis. {ECO:0000250}.

Recessive Scores

• pRec: 0.0901

Intolerance Scores

• rvis_EVS: -0.42
• rvis_percentile_EVS: 25.64

Haploinsufficiency Scores

• pHI: 0.194
• hipred: N
• hipred_score: 0.170
• ghis: 0.537

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: M1ap
• Phenotype: reproductive system phenotype; homeostasis/metabolism phenotype; cellular phenotype; endocrine/exocrine gland phenotype

Gene ontology

• Biological process: RNA processing;meiosis I;spermatogenesis;female gamete generation;cell differentiation;chromatin assembly;male meiosis chromosome separation
• Cellular component: cytoplasm;integral component of membrane
• Molecular function: molecular_function;protein binding;identical protein binding