IQCF2

IQ motif containing F2

Basic information

Region (hg38): 3:51861615-51863424

Links

ENSG00000184345 ∙ NCBI:389123 ∙ ∙ HGNC:31815 ∙ Uniprot:Q8IXL9 ∙ 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 IQCF2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQCF2 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			11	2		13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	2	0

Variants in IQCF2

This is a list of pathogenic ClinVar variants found in the IQCF2 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-51861679-T-C		not specified	Uncertain significance (Sep 14, 2022)
3-51861907-T-C		not specified	Likely benign (May 17, 2023)
3-51863017-G-C		not specified	Uncertain significance (Dec 13, 2022)
3-51863029-G-T		not specified	Uncertain significance (Nov 10, 2022)
3-51863050-G-A		not specified	Uncertain significance (Dec 07, 2024)
3-51863069-A-G		not specified	Uncertain significance (Jan 18, 2025)
3-51863098-T-G		not specified	Uncertain significance (Apr 24, 2024)
3-51863104-T-A		not specified	Uncertain significance (Sep 06, 2022)
3-51863107-C-T		not specified	Uncertain significance (Jun 11, 2021)
3-51863111-T-C		not specified	Uncertain significance (Dec 10, 2024)
3-51863120-C-T		not specified	Likely benign (Sep 17, 2021)
3-51863162-A-G		not specified	Uncertain significance (Sep 01, 2021)
3-51863207-G-A		not specified	Uncertain significance (Dec 19, 2022)
3-51863239-G-A		not specified	Uncertain significance (Aug 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQCF2	protein_coding	protein_coding	ENST00000333127	3	1796

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00124	0.863	125733	0	15	125748	0.0000596

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.391	83	93.6	0.886	0.00000576	1061
Missense in Polyphen		35	36.115	0.96913		419
Synonymous	-0.380	37	34.2	1.08	0.00000190	315
Loss of Function	1.29	6	10.5	0.571	6.06e-7	94

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000120	0.000119
Ashkenazi Jewish	0.00	0.00
East Asian	0.000109	0.000109
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.000109	0.000109
South Asian	0.000131	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.703
• rvis_EVS: 0.5
• rvis_percentile_EVS: 79.89

Haploinsufficiency Scores

• pHI: 0.160
• 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: 0.114

Gene Damage Prediction

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

Gene ontology

• Molecular function: protein binding;calmodulin binding