PFN4

profilin family member 4, the group of Profilins

Basic information

Region (hg38): 2:24114809-24123464

Links

ENSG00000176732 ∙ NCBI:375189 ∙ OMIM:620046 ∙ HGNC:31103 ∙ Uniprot:Q8NHR9 ∙ 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 PFN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PFN4 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			7	1		8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	1	0

Variants in PFN4

This is a list of pathogenic ClinVar variants found in the PFN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-24115598-T-G		not specified	Uncertain significance (Jun 23, 2023)
2-24119619-C-T		not specified	Likely benign (Feb 26, 2024)
2-24119670-C-T		not specified	Uncertain significance (Dec 04, 2024)
2-24121173-T-C		not specified	Uncertain significance (Jan 18, 2025)
2-24121195-G-A		not specified	Uncertain significance (Jan 23, 2024)
2-24121239-C-A		not specified	Uncertain significance (Dec 03, 2024)
2-24121290-C-A		not specified	Uncertain significance (Sep 24, 2024)
2-24122422-G-T		not specified	Uncertain significance (Dec 09, 2023)
2-24122472-C-A		not specified	Uncertain significance (Apr 19, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PFN4	protein_coding	protein_coding	ENST00000313213	4	8107

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00169	0.720	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0188	70	70.4	0.994	0.00000365	813
Missense in Polyphen		23	23.212	0.99085		268
Synonymous	0.279	24	25.8	0.930	0.00000119	249
Loss of Function	0.820	5	7.41	0.675	4.81e-7	86

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.00	0.00
East Asian	0.000381	0.000381
Finnish	0.00	0.00
European (Non-Finnish)	0.0000616	0.0000615
Middle Eastern	0.000381	0.000381
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Binds to phosphatidylinositol 3-phosphate (PtdIns(3)P), phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), phosphatidylinositol 4-phosphate (PtdIns(4)P) and phosphatidic acid (PA). Does not bind to actin (PubMed:19419568), contrary to other family members. {ECO:0000269|PubMed:19419568}.
• Pathway: Salmonella infection - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Rap1 signaling pathway - Homo sapiens (human);Shigellosis - Homo sapiens (human);Association Between Physico-Chemical Features and Toxicity Associated Pathways (Consensus)

Recessive Scores

• pRec: 0.114

Intolerance Scores

• loftool: 0.455
• rvis_EVS: 0.04
• rvis_percentile_EVS: 56.64

Haploinsufficiency Scores

• pHI: 0.108
• hipred: Y
• hipred_score: 0.501
• ghis: 0.461

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.219

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Pfn4

Gene ontology

• Biological process: sequestering of actin monomers
• Cellular component: cytoskeleton;cell cortex
• Molecular function: actin monomer binding;lipid binding