HCFC2

host cell factor C2

Basic information

Region (hg38): 12:104064531-104106524

Links

ENSG00000111727 ∙ NCBI:29915 ∙ OMIM:607926 ∙ HGNC:24972 ∙ Uniprot:Q9Y5Z7 ∙ 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 HCFC2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HCFC2 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			32	2		34
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	32	2	0

Variants in HCFC2

This is a list of pathogenic ClinVar variants found in the HCFC2 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-104064575-C-A		not specified	Uncertain significance (Sep 16, 2021)
12-104064720-A-T		not specified	Uncertain significance (May 24, 2023)
12-104066188-C-T		not specified	Uncertain significance (Aug 17, 2022)
12-104066297-T-A		not specified	Uncertain significance (Dec 30, 2023)
12-104068037-T-C		not specified	Uncertain significance (Nov 07, 2023)
12-104068038-A-G		not specified	Uncertain significance (Nov 13, 2024)
12-104079486-C-T		not specified	Uncertain significance (Aug 27, 2024)
12-104079582-G-C		not specified	Uncertain significance (Jan 15, 2025)
12-104080772-A-G		not specified	Uncertain significance (Sep 10, 2024)
12-104082556-C-T		not specified	Uncertain significance (Jun 10, 2024)
12-104082748-C-G		not specified	Uncertain significance (Dec 04, 2024)
12-104082805-A-T		not specified	Uncertain significance (Aug 27, 2024)
12-104082808-G-A		not specified	Uncertain significance (Sep 18, 2024)
12-104086856-C-T		not specified	Uncertain significance (Oct 02, 2023)
12-104086858-G-A		not specified	Uncertain significance (Jun 24, 2022)
12-104086898-C-A		not specified	Uncertain significance (Mar 20, 2024)
12-104086958-C-T		not specified	Uncertain significance (Nov 08, 2024)
12-104086987-G-T		not specified	Uncertain significance (Nov 01, 2022)
12-104087008-A-G		not specified	Uncertain significance (Jan 22, 2025)
12-104088015-A-T		not specified	Uncertain significance (Nov 26, 2024)
12-104088016-G-T		not specified	Uncertain significance (Dec 13, 2023)
12-104088027-G-A		not specified	Likely benign (Mar 20, 2024)
12-104093400-A-G		not specified	Likely benign (Dec 01, 2022)
12-104093474-C-T		not specified	Uncertain significance (Feb 12, 2024)
12-104093506-G-A		not specified	Uncertain significance (Jan 30, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HCFC2	protein_coding	protein_coding	ENST00000229330	15	40405

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000109	125715	0	6	125721	0.0000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.50	218	420	0.519	0.0000201	5142
Missense in Polyphen		69	187.77	0.36746		2284
Synonymous	1.81	120	148	0.811	0.00000710	1565
Loss of Function	5.36	3	39.2	0.0766	0.00000192	489

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000103	0.0000992
East Asian	0.000218	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.00000880	0.00000879
Middle Eastern	0.000218	0.000217
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Pathway: Herpes simplex infection - Homo sapiens (human) (Consensus)

Recessive Scores

• pRec: 0.200

Intolerance Scores

• loftool: 0.348
• rvis_EVS: 0.08
• rvis_percentile_EVS: 60.31

Haploinsufficiency Scores

• pHI: 0.541
• hipred: Y
• hipred_score: 0.729
• ghis: 0.519

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.946

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hcfc2
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); immune system phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: negative regulation of transcription by RNA polymerase II;regulation of transcription by RNA polymerase II;viral process;positive regulation of nucleic acid-templated transcription
• Cellular component: nucleus;nucleoplasm;cytoplasm;cytosol;plasma membrane;MLL1 complex
• Molecular function: transcription coactivator activity