HCFC1R1

host cell factor C1 regulator 1

Basic information

Region (hg38): 16:3022625-3024286

Links

ENSG00000103145 ∙ NCBI:54985 ∙ OMIM:618818 ∙ HGNC:21198 ∙ Uniprot:Q9NWW0 ∙ 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 HCFC1R1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the HCFC1R1 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in HCFC1R1

This is a list of pathogenic ClinVar variants found in the HCFC1R1 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-3022868-G-C		not specified	Uncertain significance (Nov 13, 2024)
16-3022913-G-A		not specified	Uncertain significance (Aug 01, 2024)
16-3022936-C-A		not specified	Uncertain significance (Jun 03, 2024)
16-3022936-C-T		not specified	Uncertain significance (May 23, 2023)
16-3022942-G-A		not specified	Uncertain significance (Feb 19, 2025)
16-3022963-G-A		not specified	Uncertain significance (Feb 22, 2023)
16-3022969-C-T		not specified	Uncertain significance (Sep 27, 2021)
16-3022981-A-G		not specified	Uncertain significance (Jul 08, 2022)
16-3023264-T-C		not specified	Uncertain significance (Oct 06, 2021)
16-3023267-G-T		not specified	Uncertain significance (Mar 31, 2024)
16-3023270-G-A		not specified	Uncertain significance (Mar 07, 2025)
16-3023315-G-T		not specified	Uncertain significance (Apr 06, 2024)
16-3023335-G-A		not specified	Uncertain significance (May 27, 2022)
16-3023508-G-A		not specified	Uncertain significance (Aug 04, 2023)
16-3023523-G-C		not specified	Uncertain significance (Jun 21, 2023)
16-3023895-T-A		not specified	Uncertain significance (Jan 24, 2025)
16-3023898-G-A		not specified	Uncertain significance (Oct 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
HCFC1R1	protein_coding	protein_coding	ENST00000248089	4	1667

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000593	0.496	125157	0	5	125162	0.0000200

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.526	84	71.5	1.17	0.00000347	860
Missense in Polyphen		29	24.906	1.1644		325
Synonymous	-0.371	30	27.5	1.09	0.00000119	291
Loss of Function	0.237	5	5.61	0.892	2.43e-7	62

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000330	0.0000330
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000292	0.0000265
Middle Eastern	0.00	0.00
South Asian	0.0000340	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulates HCFC1 activity by modulating its subcellular localization. Overexpression of HCFC1R1 leads to accumulation of HCFC1 in the cytoplasm. HCFC1R1-mediated export may provide the pool of cytoplasmic HCFC1 required for import of virion-derived VP16 into the nucleus. {ECO:0000269|PubMed:12235138}.

Recessive Scores

• pRec: 0.102

Intolerance Scores

• loftool: 0.692
• rvis_EVS: 0.46
• rvis_percentile_EVS: 78.16

Haploinsufficiency Scores

• pHI: 0.180
• hipred: N
• hipred_score: 0.146
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.933

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Hcfc1r1

Gene ontology

• Cellular component: nucleoplasm;cytoplasm