HORMAD2

HORMA domain containing 2

Basic information

Region (hg38): 22:30080463-30177075

Links

ENSG00000176635 ∙ NCBI:150280 ∙ OMIM:618842 ∙ HGNC:28383 ∙ Uniprot:Q8N7B1 ∙ 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 HORMAD2 gene.

• Inborn genetic diseases (8 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HORMAD2 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			7	1	1	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	7	1	1

Variants in HORMAD2

This is a list of pathogenic ClinVar variants found in the HORMAD2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-30098852-G-A		not specified	Uncertain significance (Feb 21, 2024)
22-30098858-G-C			Benign (Aug 28, 2018)
22-30098918-G-T		not specified	Uncertain significance (Jan 18, 2022)
22-30098952-G-T		not specified	Uncertain significance (Sep 25, 2023)
22-30121781-A-G		not specified	Uncertain significance (Dec 27, 2023)
22-30122008-A-T		not specified	Uncertain significance (Aug 23, 2021)
22-30122020-C-G		not specified	Uncertain significance (Apr 05, 2023)
22-30122122-G-T		not specified	Uncertain significance (Nov 15, 2023)
22-30122143-C-T		not specified	Uncertain significance (Oct 14, 2023)
22-30122153-G-A		not specified	Uncertain significance (Dec 08, 2023)
22-30122176-G-A		not specified	Uncertain significance (Dec 19, 2022)
22-30176084-T-C		not specified	Uncertain significance (Jun 28, 2022)
22-30176135-C-T		not specified	Uncertain significance (Sep 01, 2021)
22-30176156-A-G		not specified	Likely benign (May 17, 2023)
22-30176163-A-G		not specified	Uncertain significance (Apr 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HORMAD2	protein_coding	protein_coding	ENST00000336726	10	96902

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000714	0.920	124325	2	253	124580	0.00102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.627	128	150	0.856	0.00000717	2043
Missense in Polyphen		37	53.098	0.69682		739
Synonymous	-0.143	53	51.7	1.03	0.00000249	526
Loss of Function	1.61	9	15.9	0.565	8.46e-7	214

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00118	0.00115
Ashkenazi Jewish	0.00	0.00
East Asian	0.00355	0.00346
Finnish	0.00	0.00
European (Non-Finnish)	0.000711	0.000593
Middle Eastern	0.00355	0.00346
South Asian	0.00296	0.00281
Other	0.00181	0.00166

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Essential for synapsis surveillance during meiotic prophase via the recruitment of ATR activity. 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. Required for the DNA double-strand break-independent, BRCA1-dependent activation of ATR on the sex chromosomes that is essential for normal sex body formation (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.0945

Intolerance Scores

• loftool: 0.785
• rvis_EVS: 0.93
• rvis_percentile_EVS: 89.7

Haploinsufficiency Scores

• pHI: 0.147
• hipred: N
• hipred_score: 0.247

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.260

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hormad2
• Phenotype: cellular phenotype; endocrine/exocrine gland phenotype; reproductive system phenotype

Gene ontology

• Biological process: meiotic sister chromatid cohesion;meiotic cell cycle
• Cellular component: synaptonemal complex;nucleus;chromosome