IQCF1

IQ motif containing F1

Basic information

Region (hg38): 3:51894875-51903353

Links

ENSG00000173389 ∙ NCBI:132141 ∙ ∙ HGNC:28607 ∙ Uniprot:Q8N6M8 ∙ 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 IQCF1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQCF1 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 IQCF1

This is a list of pathogenic ClinVar variants found in the IQCF1 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-51894906-A-T		not specified	Uncertain significance (Jun 06, 2023)
3-51894993-T-C		not specified	Uncertain significance (Dec 21, 2023)
3-51895027-G-A		not specified	Uncertain significance (Feb 21, 2024)
3-51895053-C-A		not specified	Uncertain significance (Nov 21, 2023)
3-51895068-A-C		not specified	Uncertain significance (Feb 27, 2023)
3-51895086-C-T		not specified	Uncertain significance (Aug 10, 2021)
3-51895087-G-A		not specified	Uncertain significance (Dec 15, 2023)
3-51895099-T-G		not specified	Uncertain significance (May 27, 2022)
3-51895168-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-51895200-C-T		not specified	Uncertain significance (May 27, 2022)
3-51895255-G-A		not specified	Uncertain significance (Nov 02, 2023)
3-51895281-T-A		not specified	Uncertain significance (May 03, 2023)
3-51895299-G-A		not specified	Likely benign (Apr 25, 2022)
3-51895306-T-C		not specified	Uncertain significance (Oct 13, 2023)
3-51895315-G-A		not specified	Uncertain significance (Sep 20, 2023)
3-51896882-C-A		not specified	Uncertain significance (Dec 19, 2023)
3-51896889-T-G		not specified	Uncertain significance (Jul 30, 2023)
3-51896890-T-G		not specified	Uncertain significance (Jun 17, 2022)
3-51902989-G-T		not specified	Uncertain significance (Jan 29, 2024)
3-51903067-G-A		not specified	Uncertain significance (Feb 03, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQCF1	protein_coding	protein_coding	ENST00000310914	4	8460

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00112	0.848	125739	0	9	125748	0.0000358

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.313	130	120	1.08	0.00000773	1311
Missense in Polyphen		38	38.014	0.99964		439
Synonymous	1.34	33	44.3	0.745	0.00000228	412
Loss of Function	1.24	6	10.3	0.583	4.43e-7	120

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000617	0.0000615
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Involved in sperm capacitation and acrosome reaction. {ECO:0000250|UniProtKB:Q9D9K8}.

Intolerance Scores

• loftool: 0.521
• rvis_EVS: 0.64
• rvis_percentile_EVS: 83.78

Haploinsufficiency Scores

• pHI: 0.0807
• hipred: N
• hipred_score: 0.112
• ghis: 0.414

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0929

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Iqcf1
• Phenotype: reproductive system phenotype; cellular phenotype

Gene ontology

• Biological process: positive regulation of flagellated sperm motility involved in capacitation;positive regulation of acrosome reaction
• Cellular component: acrosomal vesicle
• Molecular function: calmodulin binding