IHO1

interactor of HORMAD1 1

Basic information

Region (hg38): 3:49198428-49258106

Previous symbols: [ "CCDC36" ]

Links

ENSG00000173421 ∙ NCBI:339834 ∙ OMIM:619190 ∙ HGNC:27945 ∙ Uniprot:Q8IYA8 ∙ 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 IHO1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IHO1 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			23			23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	0	0

Variants in IHO1

This is a list of pathogenic ClinVar variants found in the IHO1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-49236660-G-T		not specified	Uncertain significance (Oct 10, 2023)
3-49241236-G-A		not specified	Uncertain significance (Jul 10, 2024)
3-49241274-G-A		not specified	Uncertain significance (Nov 11, 2024)
3-49241285-A-G		not specified	Uncertain significance (Apr 12, 2024)
3-49241359-A-G		not specified	Uncertain significance (Sep 20, 2024)
3-49241388-A-G		not specified	Uncertain significance (Nov 20, 2023)
3-49244440-A-C		not specified	Uncertain significance (Jan 06, 2023)
3-49244665-A-G		not specified	Uncertain significance (Aug 28, 2024)
3-49255395-G-C		not specified	Uncertain significance (May 13, 2024)
3-49255483-G-C		not specified	Uncertain significance (Oct 03, 2022)
3-49256176-C-T		not specified	Uncertain significance (Nov 08, 2024)
3-49256196-G-T		not specified	Uncertain significance (Jan 23, 2023)
3-49256249-C-T		not specified	Uncertain significance (Oct 05, 2021)
3-49256258-T-G		not specified	Uncertain significance (May 16, 2023)
3-49256282-C-T		not specified	Uncertain significance (Mar 11, 2022)
3-49256315-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-49256318-C-T		not specified	Uncertain significance (Dec 21, 2023)
3-49256417-A-T		not specified	Uncertain significance (Feb 10, 2022)
3-49256498-C-T		not specified	Uncertain significance (Apr 12, 2023)
3-49256509-G-A		not specified	Uncertain significance (Apr 24, 2024)
3-49256521-C-T		not specified	Uncertain significance (Jan 06, 2023)
3-49256591-C-T		not specified	Uncertain significance (Jan 26, 2022)
3-49256606-A-G		not specified	Uncertain significance (Dec 22, 2023)
3-49256617-G-A		not specified	Likely benign (Sep 26, 2024)
3-49256620-C-G		not specified	Uncertain significance (Aug 11, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IHO1	protein_coding	protein_coding	ENST00000438782	7	59677

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0245	0.963	125735	0	10	125745	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.01	245	294	0.834	0.0000138	3937
Missense in Polyphen		45	64.928	0.69308		1019
Synonymous	1.31	94	112	0.842	0.00000540	1095
Loss of Function	2.19	5	13.8	0.363	5.83e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000129	0.000123
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000545	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for DNA double-strand breaks (DSBs) formation in unsynapsed regions during meiotic recombination. Probably acts by forming a complex with MEI4 and REC114, which activates DSBs formation in unsynapsed regions, an essential step to ensure completion of synapsis. Not required for HORMAD1 functions in pairing-independent synaptonemal complex formation, ATR recruitment to unsynapsed axes, meiotic silencing of unsynapsed chromatin (MSUC) or meiotic surveillance. {ECO:0000250|UniProtKB:Q6PDM4}.

Intolerance Scores

• loftool: 0.878
• rvis_EVS: -0.51
• rvis_percentile_EVS: 21.56

Haploinsufficiency Scores

• pHI: 0.0889
• hipred: N
• hipred_score: 0.273
• ghis: 0.515

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0397

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ccdc36

Gene ontology

• Biological process: DNA recombination;synapsis;spermatogenesis;meiotic DNA double-strand break formation;oogenesis;regulation of homologous chromosome segregation
• Cellular component: condensed nuclear chromosome
• Molecular function: protein binding