PHETA2

PH domain containing endocytic trafficking adaptor 2, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 22:42074248-42079438

Previous symbols: [ "FAM109B" ]

Links

ENSG00000177096 ∙ NCBI:150368 ∙ OMIM:614240 ∙ HGNC:27161 ∙ Uniprot:Q6ICB4 ∙ 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 PHETA2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHETA2 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			22	1		23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	1	0

Variants in PHETA2

This is a list of pathogenic ClinVar variants found in the PHETA2 region.

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

Position	Type	Phenotype	Significance	ClinVar
22-42077316-T-G		not specified	Uncertain significance (Dec 10, 2024)
22-42077336-G-A		not specified	Uncertain significance (Feb 28, 2024)
22-42077394-C-T		not specified	Uncertain significance (Apr 20, 2024)
22-42077406-G-C		not specified	Uncertain significance (Jan 29, 2024)
22-42077415-G-A		not specified	Uncertain significance (Jun 04, 2024)
22-42077499-T-C		not specified	Uncertain significance (Jul 20, 2021)
22-42077510-A-G		not specified	Uncertain significance (Dec 01, 2022)
22-42077567-G-T		not specified	Uncertain significance (Jun 22, 2024)
22-42077579-G-A		not specified	Uncertain significance (Jan 15, 2025)
22-42077610-C-T		not specified	Uncertain significance (May 25, 2023)
22-42077646-G-A		not specified	Uncertain significance (Jun 07, 2023)
22-42077666-C-A		not specified	Uncertain significance (Aug 04, 2023)
22-42077667-G-A		not specified	Uncertain significance (Feb 17, 2024)
22-42077679-G-A		not specified	Uncertain significance (Aug 28, 2024)
22-42077689-G-C		not specified	Uncertain significance (May 23, 2023)
22-42077709-G-A		not specified	Uncertain significance (Dec 03, 2021)
22-42077718-T-C		not specified	Uncertain significance (Mar 28, 2024)
22-42077729-C-T		not specified	Uncertain significance (Feb 21, 2024)
22-42077730-G-A		not specified	Uncertain significance (Jan 31, 2023)
22-42077759-C-T		not specified	Uncertain significance (Mar 01, 2023)
22-42077834-C-A		not specified	Uncertain significance (Sep 13, 2023)
22-42077856-C-T		not specified	Uncertain significance (Apr 19, 2024)
22-42077909-G-A		not specified	Uncertain significance (Aug 30, 2021)
22-42077999-G-A		not specified	Likely benign (Jan 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHETA2	protein_coding	protein_coding	ENST00000321753	1	5191

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000339	0.204	125530	1	204	125735	0.000816

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.825	132	162	0.817	0.0000103	1653
Missense in Polyphen		61	64.541	0.94514		680
Synonymous	0.858	60	69.1	0.869	0.00000424	555
Loss of Function	-0.203	8	7.40	1.08	4.88e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00775	0.00756
Ashkenazi Jewish	0.000123	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.00225	0.00222
European (Non-Finnish)	0.000179	0.000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000654	0.0000653
Other	0.000519	0.000489

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Plays a role in endocytic trafficking. Required for receptor recycling from endosomes, both to the trans-Golgi network and the plasma membrane. {ECO:0000269|PubMed:21233288}.

Intolerance Scores

• rvis_EVS: 0.19
• rvis_percentile_EVS: 67.03

Haploinsufficiency Scores

• pHI: 0.0973
• hipred: N
• hipred_score: 0.178
• ghis: 0.501

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pheta2

Gene ontology

• Biological process: receptor recycling;endosome organization;retrograde transport, endosome to Golgi
• Cellular component: early endosome;trans-Golgi network;cytosol;clathrin-coated vesicle;recycling endosome
• Molecular function: protein binding;protein homodimerization activity