PHACTR2

phosphatase and actin regulator 2, the group of Phosphatase and actin regulators

Basic information

Region (hg38): 6:143536844-143831185

Previous symbols: [ "C6orf56" ]

Links

ENSG00000112419 ∙ NCBI:9749 ∙ OMIM:608724 ∙ HGNC:20956 ∙ Uniprot:O75167 ∙ 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 PHACTR2 gene.

• Inborn genetic diseases (24 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHACTR2 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			24			24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	24	0	0

Variants in PHACTR2

This is a list of pathogenic ClinVar variants found in the PHACTR2 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-143712030-A-C		not specified	Uncertain significance (May 17, 2023)
6-143712076-C-G		not specified	Uncertain significance (Aug 12, 2021)
6-143753894-C-G		not specified	Uncertain significance (Apr 25, 2022)
6-143760409-G-A		not specified	Uncertain significance (Jan 22, 2024)
6-143760423-A-C		not specified	Uncertain significance (Sep 29, 2023)
6-143760433-G-A		not specified	Uncertain significance (Aug 14, 2023)
6-143760448-C-G		not specified	Uncertain significance (Jul 17, 2023)
6-143760467-C-T		not specified	Uncertain significance (Aug 16, 2022)
6-143760592-C-A		not specified	Uncertain significance (Jun 02, 2023)
6-143760605-C-T		not specified	Uncertain significance (Aug 17, 2022)
6-143760626-C-T		not specified	Uncertain significance (Feb 23, 2023)
6-143765288-C-T		not specified	Uncertain significance (Oct 13, 2023)
6-143765336-G-A		not specified	Uncertain significance (Dec 28, 2022)
6-143765344-G-A		not specified	Uncertain significance (Aug 05, 2023)
6-143765345-C-G		not specified	Uncertain significance (Aug 05, 2023)
6-143765438-C-G		not specified	Uncertain significance (Jan 27, 2022)
6-143765475-A-T		not specified	Uncertain significance (Oct 17, 2023)
6-143765507-T-G		not specified	Uncertain significance (Dec 16, 2023)
6-143765516-A-G		not specified	Uncertain significance (Mar 23, 2022)
6-143765528-C-T		not specified	Uncertain significance (Jan 03, 2024)
6-143765581-C-G		not specified	Uncertain significance (Mar 01, 2024)
6-143765611-C-T		not specified	Uncertain significance (Sep 14, 2022)
6-143765642-C-T		not specified	Uncertain significance (Sep 20, 2023)
6-143765660-T-C		not specified	Uncertain significance (Jan 12, 2024)
6-143765660-T-G		not specified	Uncertain significance (Apr 17, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHACTR2	protein_coding	protein_coding	ENST00000440869	13	294341

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000104	0.999	124759	0	33	124792	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.813	299	341	0.876	0.0000184	4142
Missense in Polyphen		120	174.46	0.68784		2211
Synonymous	-0.234	136	133	1.03	0.00000777	1315
Loss of Function	3.01	16	35.3	0.454	0.00000234	388

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000336	0.000332
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000556	0.0000556
Finnish	0.0000490	0.0000464
European (Non-Finnish)	0.000178	0.000177
Middle Eastern	0.0000556	0.0000556
South Asian	0.0000327	0.0000327
Other	0.000169	0.000165

dbNSFP

Source: dbNSFP

• Pathway: Platelet degranulation ;Response to elevated platelet cytosolic Ca2+;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.0917

Intolerance Scores

• loftool: 0.858
• rvis_EVS: -0.05
• rvis_percentile_EVS: 50.34

Haploinsufficiency Scores

• pHI: 0.727
• hipred: N
• hipred_score: 0.389
• ghis: 0.467

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00879

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Phactr2

Gene ontology

• Biological process: platelet degranulation;negative regulation of phosphoprotein phosphatase activity
• Cellular component: plasma membrane;platelet alpha granule membrane
• Molecular function: actin binding;protein phosphatase inhibitor activity;protein binding