IQCF3

IQ motif containing F3

Basic information

Region (hg38): 3:51826882-51833389

Links

ENSG00000229972 ∙ NCBI:401067 ∙ ∙ HGNC:31816 ∙ Uniprot:P0C7M6 ∙ 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 IQCF3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the IQCF3 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	4		15
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	4	0

Variants in IQCF3

This is a list of pathogenic ClinVar variants found in the IQCF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
3-51829684-A-G		not specified	Uncertain significance (Sep 12, 2023)
3-51829705-G-A		not specified	Likely benign (Dec 19, 2022)
3-51830448-G-A		not specified	Uncertain significance (Nov 14, 2023)
3-51830485-G-A		not specified	Uncertain significance (Feb 27, 2023)
3-51830502-G-C		not specified	Uncertain significance (Mar 12, 2024)
3-51830503-C-A		not specified	Uncertain significance (Mar 12, 2024)
3-51830542-C-T		not specified	Uncertain significance (May 24, 2024)
3-51830556-C-T		not specified	Uncertain significance (Mar 28, 2023)
3-51830557-G-A		not specified	Likely benign (Jul 09, 2021)
3-51830563-G-A		not specified	Likely benign (Sep 22, 2023)
3-51830568-C-T		not specified	Uncertain significance (Dec 15, 2023)
3-51830628-T-G		not specified	Uncertain significance (May 18, 2022)
3-51830638-G-A		not specified	Uncertain significance (Dec 07, 2021)
3-51830652-C-T		not specified	Uncertain significance (Feb 22, 2023)
3-51830665-G-A		not specified	Uncertain significance (Aug 30, 2021)
3-51830693-C-A		not specified	Likely benign (Dec 06, 2022)
3-51830701-C-T		not specified	Uncertain significance (May 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
IQCF3	protein_coding	protein_coding	ENST00000456080	3	13257

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000433	0.252	124533	0	4	124537	0.0000161

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.405	85	96.2	0.884	0.00000613	994
Missense in Polyphen		20	20.766	0.96313		215
Synonymous	-0.773	40	34.2	1.17	0.00000184	297
Loss of Function	-1.15	4	2.17	1.84	9.20e-8	25

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000938	0.0000937
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00000888	0.00000886
Middle Eastern	0.00	0.00
South Asian	0.0000371	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.513
• rvis_EVS: 0.02
• rvis_percentile_EVS: 55.22

Haploinsufficiency Scores

• hipred: N
• hipred_score: 0.112
• ghis: 0.453

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: calmodulin binding