HECA

hdc homolog, cell cycle regulator

Basic information

Region (hg38): 6:139135079-139180802

Links

ENSG00000112406 ∙ NCBI:51696 ∙ OMIM:607977 ∙ HGNC:21041 ∙ Uniprot:Q9UBI9 ∙ 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 HECA gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HECA 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			19	1		20
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	19	1	0

Variants in HECA

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

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

Position	Type	Phenotype	Significance	ClinVar
6-139135524-C-G		not specified	Uncertain significance (Dec 16, 2023)
6-139135551-C-T		not specified	Uncertain significance (May 06, 2022)
6-139135626-C-T		not specified	Uncertain significance (Mar 29, 2022)
6-139135653-G-C		not specified	Uncertain significance (Mar 04, 2024)
6-139135655-G-A		not specified	Uncertain significance (Dec 21, 2022)
6-139166319-G-A		not specified	Uncertain significance (Nov 19, 2022)
6-139166326-C-T		not specified	Uncertain significance (May 05, 2023)
6-139166457-G-A		not specified	Uncertain significance (Jun 11, 2021)
6-139166649-A-G		not specified	Uncertain significance (Nov 07, 2022)
6-139166662-A-G		not specified	Uncertain significance (Nov 05, 2021)
6-139166668-C-T		not specified	Likely benign (Nov 07, 2022)
6-139166734-G-A		not specified	Uncertain significance (Dec 30, 2023)
6-139166775-G-A		not specified	Uncertain significance (Nov 17, 2022)
6-139166838-G-A		not specified	Uncertain significance (Feb 01, 2023)
6-139166871-G-A		not specified	Uncertain significance (Jul 19, 2022)
6-139166877-C-A		not specified	Uncertain significance (May 31, 2023)
6-139166983-A-C		not specified	Uncertain significance (Feb 16, 2023)
6-139167001-C-T		not specified	Uncertain significance (Aug 30, 2021)
6-139167172-C-T		not specified	Uncertain significance (Jan 23, 2023)
6-139174408-G-A		not specified	Uncertain significance (Jun 30, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HECA	protein_coding	protein_coding	ENST00000367658	4	45691

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.615	0.385	125737	0	11	125748	0.0000437

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.61	181	310	0.583	0.0000203	3564
Missense in Polyphen		72	163.51	0.44033		1685
Synonymous	-0.466	142	135	1.05	0.0000102	1079
Loss of Function	3.02	3	16.0	0.187	6.81e-7	206

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000579	0.0000579
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000353	0.0000352
Middle Eastern	0.00	0.00
South Asian	0.0000981	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play an important role in some human cancers. May be part of the regulatory mechanism in the development of epithelial tube networks such as the circulatory system and lungs. {ECO:0000303|PubMed:11696983}.

Recessive Scores

• pRec: 0.153

Intolerance Scores

• loftool: 0.0538
• rvis_EVS: -0.67
• rvis_percentile_EVS: 15.62

Haploinsufficiency Scores

• pHI: 0.230
• hipred: N
• hipred_score: 0.476
• ghis: 0.603

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.250

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Heca

Gene ontology

• Biological process: respiratory tube development;negative regulation of mitotic cell cycle
• Cellular component: nucleus;cytoplasm;membrane
• Molecular function: molecular_function