HOOK1

hook microtubule tethering protein 1, the group of FHF complex

Basic information

Region (hg38): 1:59814786-59876322

Links

ENSG00000134709 ∙ NCBI:51361 ∙ OMIM:607820 ∙ HGNC:19884 ∙ Uniprot:Q9UJC3 ∙ 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 HOOK1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOOK1 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				2		2
missense			54	2		56
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	54	4	0

Variants in HOOK1

This is a list of pathogenic ClinVar variants found in the HOOK1 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-59815134-C-T		not specified	Uncertain significance (Oct 18, 2021)
1-59815171-C-T			Likely benign (Mar 01, 2022)
1-59815172-A-G		not specified	Uncertain significance (Jan 18, 2025)
1-59821871-A-G		not specified	Uncertain significance (Sep 13, 2023)
1-59821904-T-C		not specified	Uncertain significance (May 06, 2024)
1-59821919-C-G		not specified	Uncertain significance (Oct 06, 2024)
1-59832163-G-A		not specified	Uncertain significance (Jan 03, 2024)
1-59833409-T-G		not specified	Uncertain significance (Feb 28, 2023)
1-59833498-C-T		not specified	Uncertain significance (May 26, 2022)
1-59833534-C-G		not specified	Uncertain significance (Oct 30, 2023)
1-59836886-A-C		not specified	Uncertain significance (Aug 01, 2024)
1-59836907-A-T		not specified	Uncertain significance (Nov 08, 2022)
1-59840354-A-G		not specified	Uncertain significance (Jan 19, 2025)
1-59843438-A-G		not specified	Likely benign (Jun 06, 2023)
1-59843471-G-A		not specified	Uncertain significance (Jan 26, 2023)
1-59843476-T-G		not specified	Uncertain significance (Sep 14, 2022)
1-59843485-G-T		not specified	Uncertain significance (Mar 08, 2025)
1-59843492-A-G		not specified	Uncertain significance (Mar 05, 2024)
1-59843509-T-A		not specified	Uncertain significance (Dec 01, 2022)
1-59847070-C-T		not specified	Uncertain significance (Dec 03, 2024)
1-59847119-G-C		not specified	Uncertain significance (Dec 15, 2022)
1-59847151-A-G		not specified	Uncertain significance (Jul 14, 2021)
1-59847176-A-T		not specified	Uncertain significance (Dec 28, 2023)
1-59848347-C-T		not specified	Uncertain significance (Jun 11, 2024)
1-59848361-T-C		not specified	Uncertain significance (Nov 13, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOOK1	protein_coding	protein_coding	ENST00000371208	22	61593

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.87e-8	1.00	125703	0	40	125743	0.000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.849	318	364	0.875	0.0000186	4842
Missense in Polyphen		130	146.28	0.88871		1967
Synonymous	0.514	115	122	0.941	0.00000624	1228
Loss of Function	3.66	21	48.5	0.433	0.00000228	601

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000302	0.000301
Ashkenazi Jewish	0.00	0.00
East Asian	0.000223	0.000163
Finnish	0.0000463	0.0000462
European (Non-Finnish)	0.000254	0.000237
Middle Eastern	0.000223	0.000163
South Asian	0.0000746	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Required for spermatid differentiation. Probably involved in the positioning of the microtubules of the manchette and the flagellum in relation to the membrane skeleton (By similarity). Component of the FTS/Hook/FHIP complex (FHF complex). The FHF complex may function to promote vesicle trafficking and/or fusion via the homotypic vesicular protein sorting complex (the HOPS complex) (PubMed:18799622). {ECO:0000250|UniProtKB:Q8BIL5, ECO:0000269|PubMed:18799622}.

Recessive Scores

• pRec: 0.112

Intolerance Scores

• loftool: 0.811
• rvis_EVS: -0.62
• rvis_percentile_EVS: 17.36

Haploinsufficiency Scores

• pHI: 0.459
• hipred: Y
• hipred_score: 0.544
• ghis: 0.539

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.801

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hook1
• Phenotype: cellular phenotype; reproductive system phenotype

Gene ontology

• Biological process: Golgi organization;endosome organization;lysosome organization;multicellular organism development;endosome to lysosome transport;protein transport;cytoskeleton-dependent intracellular transport;cytoplasmic microtubule organization;early endosome to late endosome transport;manchette assembly
• Cellular component: cytoplasm;centrosome;cytosol;microtubule;HOPS complex;FHF complex
• Molecular function: actin binding;protein binding;microtubule binding;identical protein binding;dynein light intermediate chain binding