HORMAD1

HORMA domain containing 1

Basic information

Region (hg38): 1:150698060-150720895

Links

ENSG00000143452 ∙ NCBI:84072 ∙ OMIM:609824 ∙ HGNC:25245 ∙ Uniprot:Q86X24 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• male infertility with azoospermia or oligozoospermia due to single gene mutation (Moderate), mode of inheritance: AR

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the HORMAD1 gene.

• Male infertility (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HORMAD1 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			15	2	1	18
nonsense	1					1
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	1	0	15	2	1

Variants in HORMAD1

This is a list of pathogenic ClinVar variants found in the HORMAD1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-150698671-G-T		not specified	Uncertain significance (Nov 08, 2022)
1-150698697-A-C		not specified	Uncertain significance (Jan 16, 2024)
1-150698703-T-A		not specified	Uncertain significance (Jan 29, 2025)
1-150698708-A-C		not specified	Uncertain significance (Aug 02, 2022)
1-150700125-T-C		not specified	Uncertain significance (Nov 27, 2023)
1-150700143-C-T		not specified	Uncertain significance (Jan 22, 2024)
1-150700152-T-C		not specified	Uncertain significance (Dec 03, 2024)
1-150703321-G-A		Male infertility	Pathogenic (Oct 18, 2022)
1-150703356-A-T		not specified	Uncertain significance (May 01, 2024)
1-150704146-C-A		not specified	Uncertain significance (Aug 01, 2022)
1-150704170-T-C		not specified	Uncertain significance (Apr 07, 2022)
1-150704319-T-C		not specified	Uncertain significance (Apr 11, 2025)
1-150704331-T-C		not specified	Uncertain significance (Oct 06, 2022)
1-150706596-A-G		not specified	Uncertain significance (Feb 08, 2025)
1-150706599-A-G		not specified	Uncertain significance (Apr 03, 2025)
1-150706609-A-G		not specified	Likely benign (Dec 20, 2023)
1-150706639-T-C		not specified	Uncertain significance (Dec 16, 2021)
1-150706662-C-T		not specified	Uncertain significance (May 15, 2025)
1-150706668-C-T		not specified	Likely benign (Jan 18, 2023)
1-150706801-G-A		not specified	Uncertain significance (Apr 19, 2024)
1-150708340-G-A		not specified	Uncertain significance (Mar 20, 2025)
1-150708373-T-C			Benign (Jun 01, 2018)
1-150708406-T-C		not specified	Uncertain significance (Oct 07, 2024)
1-150708936-T-A		not specified	Uncertain significance (Mar 27, 2025)
1-150711564-G-A		not specified	Uncertain significance (Apr 22, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HORMAD1	protein_coding	protein_coding	ENST00000361824	14	22829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.949	0.0511	125721	0	5	125726	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.54	132	192	0.688	0.00000886	2600
Missense in Polyphen		31	68.238	0.45429		890
Synonymous	0.717	56	63.3	0.885	0.00000309	677
Loss of Function	3.82	3	22.6	0.133	0.00000105	312

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000635	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000963	0.0000924
European (Non-Finnish)	0.00000886	0.00000879
Middle Eastern	0.00	0.00
South Asian	0.0000333	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a key role in meiotic progression. Regulates 3 different functions during meiosis: ensures that sufficient numbers of processed DNA double-strand breaks (DSBs) are available for successful homology search by increasing the steady-state numbers of single-stranded DSB ends. Promotes synaptonemal-complex formation independently of its role in homology search. Plays a key role in the male mid-pachytene checkpoint and the female meiotic prophase checkpoint: required for efficient build-up of ATR activity on unsynapsed chromosome regions, a process believed to form the basis of meiotic silencing of unsynapsed chromatin (MSUC) and meiotic prophase quality control in both sexes. {ECO:0000250|UniProtKB:Q9D5T7}.

Recessive Scores

• pRec: 0.0994

Intolerance Scores

• loftool: 0.789
• rvis_EVS: 0.1
• rvis_percentile_EVS: 61.49

Haploinsufficiency Scores

• pHI: 0.344
• hipred: N
• hipred_score: 0.353
• ghis: 0.442

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0770

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hormad1
• Phenotype: endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; reproductive system phenotype; embryo phenotype

Gene ontology

• Biological process: blastocyst development;synaptonemal complex assembly;spermatogenesis;meiotic DNA double-strand break formation;oogenesis;meiotic sister chromatid cohesion;meiotic cell cycle;meiotic recombination checkpoint;regulation of homologous chromosome segregation
• Cellular component: synaptonemal complex;nucleus;chromosome