HYCC2

protein-coding

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

Gene summary

Predicted to be involved in phosphatidylinositol phosphate biosynthetic process and protein localization to plasma membrane. Located in cell junction. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

FAM126B

MANE transcript

NM_001321623.1

Inheritance

—

ClinVar variants

U:61B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.25

Max pathogenic AF

—

Genomic locus

chr2:200,973,718-201,071,671

External References & Databases

Ensembl (ENSG00000155744)

Transcript & Mutation Effects

hg38 • Region Span ~98.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to HYCC2 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 58

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001321623.1. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			57 clinvar	1 clinvar		58
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	61	1	0	62

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 112 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001321623.1	RefSeq	NP_001308552.1	11	MANE Select
ENST00000681958.1	Ensembl	ENSP00000507218.1	11	MANE Select
NM_001321618.1	RefSeq	NP_001308547.1	10	Standard
NM_001321619.2	RefSeq	NP_001308548.1	10	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

phosphatidylinositol phosphorylation
protein localization to plasma membrane

Molecular Function

protein binding

Cellular Component

cytosol
plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000418596
Coding exons: 10
Length: 97954
Individuals with no LoFs: 125723
Homozygous LoFs: 0
Heterozygous LoFs: 23
Defined: 125746
p: 0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.40	224	291	0.770	0.0000155	3420
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00018	0.00018	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0.000099	0.000099	rare
East Asian	0	0.0	absent
Finnish	0.000092	0.000092	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.00023	0.00020	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.307

Gene Damage Prediction

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