HOOK2

hook microtubule tethering protein 2, the group of FHF complex

Basic information

Region (hg38): 19:12763002-12872740

Links

ENSG00000095066 ∙ NCBI:29911 ∙ OMIM:607824 ∙ HGNC:19885 ∙ Uniprot:Q96ED9 ∙ 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 HOOK2 gene.

• Inborn genetic diseases (39 variants)
• not provided (4 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HOOK2 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			38	2	2	42
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	0	0	38	2	2

Variants in HOOK2

This is a list of pathogenic ClinVar variants found in the HOOK2 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-12763340-C-G		not specified	Uncertain significance (Mar 31, 2023)
19-12763359-G-A		not specified	Uncertain significance (Jun 24, 2022)
19-12763379-T-G		not specified	Uncertain significance (May 18, 2023)
19-12763392-G-A		not specified	Uncertain significance (Dec 21, 2021)
19-12763397-C-T		not specified	Uncertain significance (May 04, 2022)
19-12763412-C-T		not specified	Uncertain significance (Jun 18, 2021)
19-12763569-C-T			Likely benign (Jun 08, 2018)
19-12763571-C-T		not specified	Uncertain significance (May 05, 2023)
19-12763572-G-A		not specified	Uncertain significance (Sep 27, 2021)
19-12763684-C-T		not specified	Uncertain significance (Dec 03, 2021)
19-12763685-G-A		not specified	Uncertain significance (Mar 06, 2023)
19-12763693-C-T		not specified	Uncertain significance (Nov 08, 2022)
19-12763699-C-T		not specified	Uncertain significance (Jan 09, 2024)
19-12763768-G-A		not specified	Uncertain significance (Dec 07, 2021)
19-12764906-T-G		not specified	Uncertain significance (Aug 12, 2021)
19-12765697-C-T		not specified	Uncertain significance (Aug 04, 2021)
19-12765945-C-G		not specified	Uncertain significance (Apr 13, 2022)
19-12765970-T-C		not specified	Uncertain significance (Jul 06, 2021)
19-12766107-G-A		not specified	Uncertain significance (Aug 02, 2023)
19-12766107-G-T		not specified	Uncertain significance (Dec 02, 2021)
19-12766150-G-C			Benign (Oct 29, 2020)
19-12767435-C-G			Benign (Nov 10, 2017)
19-12767876-G-A		not specified	Uncertain significance (Nov 30, 2022)
19-12767903-G-A		not specified	Uncertain significance (May 09, 2023)
19-12768065-A-T		not specified	Uncertain significance (Dec 27, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HOOK2	protein_coding	protein_coding	ENST00000397668	23	109738

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.65e-18	0.691	125481	0	102	125583	0.000406

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.371	429	451	0.951	0.0000303	4578
Missense in Polyphen		113	103.32	1.0937		1224
Synonymous	0.794	174	188	0.926	0.0000118	1421
Loss of Function	1.98	35	50.2	0.698	0.00000265	528

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00101	0.000988
Ashkenazi Jewish	0.00	0.00
East Asian	0.000891	0.000875
Finnish	0.0000466	0.0000463
European (Non-Finnish)	0.000466	0.000457
Middle Eastern	0.000891	0.000875
South Asian	0.000196	0.000196
Other	0.000331	0.000327

dbNSFP

Source: dbNSFP

• Function: FUNCTION: 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). Contributes to the establishment and maintenance of centrosome function. May function in the positioning or formation of aggresomes, which are pericentriolar accumulations of misfolded proteins, proteasomes and chaperones. {ECO:0000269|PubMed:17140400, ECO:0000269|PubMed:17540036, ECO:0000269|PubMed:18799622}.

Recessive Scores

• pRec: 0.107

Intolerance Scores

• loftool: 0.932
• rvis_EVS: 0.31
• rvis_percentile_EVS: 72.75

Haploinsufficiency Scores

• pHI: 0.101
• hipred: Y
• hipred_score: 0.523
• ghis: 0.498

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.961

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hook2

Gene ontology

• Biological process: endocytosis;endosome organization;lysosome organization;endosome to lysosome transport;protein transport;cytoskeleton-dependent intracellular transport;cytoplasmic microtubule organization;early endosome to late endosome transport
• Cellular component: cytoplasm;centrosome;cytosol;microtubule;HOPS complex;intracellular membrane-bounded organelle;FHF complex
• Molecular function: protein binding;microtubule binding;identical protein binding;dynein light intermediate chain binding