HYCC2

hyccin PI4KA lipid kinase complex subunit 2, the group of PI4KA lipid kinase complex

Basic information

Region (hg38): 2:200973717-201071671

Previous symbols: [ "FAM126B" ]

Links

ENSG00000155744 ∙ NCBI:285172 ∙ ∙ HGNC:28593 ∙ Uniprot:Q8IXS8 ∙ 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 HYCC2 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HYCC2 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			5	1		6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	5	1	0

Variants in HYCC2

This is a list of pathogenic ClinVar variants found in the HYCC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-200981359-C-T		not specified	Uncertain significance (Sep 29, 2023)
2-200981406-C-T		not specified	Uncertain significance (Dec 20, 2023)
2-200981496-G-A		not specified	Uncertain significance (Dec 06, 2022)
2-200981560-G-C		not specified	Uncertain significance (Sep 01, 2021)
2-200981590-T-C		not specified	Uncertain significance (Feb 28, 2024)
2-200981646-T-C		not specified	Likely benign (Mar 02, 2023)
2-200981650-G-A		not specified	Uncertain significance (Feb 11, 2022)
2-200981659-A-C		not specified	Uncertain significance (Nov 03, 2023)
2-200981670-C-G		not specified	Uncertain significance (Aug 28, 2023)
2-200988282-C-T		not specified	Uncertain significance (Feb 13, 2024)
2-200988382-G-C		not specified	Uncertain significance (Feb 13, 2023)
2-200992917-A-G		not specified	Uncertain significance (Feb 16, 2023)
2-200992980-C-T		not specified	Uncertain significance (Feb 23, 2023)
2-200997511-C-T		not specified	Uncertain significance (Jan 31, 2024)
2-200997514-A-T		not specified	Uncertain significance (Oct 27, 2021)
2-201009066-G-A		not specified	Uncertain significance (Nov 14, 2023)
2-201011423-G-A		not specified	Uncertain significance (Dec 09, 2023)
2-201011466-C-A		not specified	Uncertain significance (Dec 21, 2021)
2-201017022-A-G		not specified	Uncertain significance (Jan 23, 2024)
2-201017115-C-T		not specified	Uncertain significance (Feb 28, 2023)
2-201017133-T-C		not specified	Uncertain significance (Jul 28, 2021)
2-201017158-C-G		not specified	Uncertain significance (Feb 27, 2023)
2-201022833-C-T		not specified	Uncertain significance (Sep 27, 2021)
2-201022886-C-T		not specified	Uncertain significance (Sep 27, 2022)
2-201023971-T-A		not specified	Uncertain significance (Mar 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HYCC2	protein_coding	protein_coding	ENST00000418596	10	97954

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.179	0.821	125723	0	23	125746	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.40	224	291	0.770	0.0000155	3420
Missense in Polyphen		81	122.9	0.65908		1528
Synonymous	1.34	83	100	0.830	0.00000445	1076
Loss of Function	3.71	7	28.3	0.247	0.00000162	325

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000243	0.000242
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.000231	0.000196
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Component of a complex required to localize phosphatidylinositol 4-kinase (PI4K) to the plasma membrane. {ECO:0000305|PubMed:26571211}.

Intolerance Scores

• loftool: 0.394
• rvis_EVS: -0.43
• rvis_percentile_EVS: 25.37

Haploinsufficiency Scores

• pHI: 0.135
• hipred: Y
• hipred_score: 0.699
• ghis: 0.643

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Fam126b

Gene ontology

• Biological process: phosphatidylinositol phosphorylation;protein localization to plasma membrane
• Cellular component: cytosol;plasma membrane
• Molecular function: protein binding