PHETA1

PH domain containing endocytic trafficking adaptor 1, the group of Pleckstrin homology domain containing

Basic information

Region (hg38): 12:111360651-111369121

Previous symbols: [ "FAM109A" ]

Links

ENSG00000198324 ∙ NCBI:144717 ∙ OMIM:614239 ∙ HGNC:26509 ∙ Uniprot:Q8N4B1 ∙ 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 PHETA1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the PHETA1 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			28	1		29
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	29	1	0

Variants in PHETA1

This is a list of pathogenic ClinVar variants found in the PHETA1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-111362712-C-T		not specified	Uncertain significance (Jul 25, 2023)
12-111362721-C-T		not specified	Uncertain significance (Nov 15, 2021)
12-111362722-G-A		not specified	Uncertain significance (Oct 26, 2021)
12-111362751-C-T		not specified	Likely benign (Jul 09, 2021)
12-111362752-G-A		not specified	Uncertain significance (Feb 03, 2025)
12-111362766-A-G		not specified	Uncertain significance (Jul 28, 2021)
12-111362797-G-A		not specified	Uncertain significance (May 08, 2024)
12-111362803-G-A		not specified	Uncertain significance (Jun 26, 2024)
12-111362808-G-A		not specified	Uncertain significance (Nov 14, 2024)
12-111362827-G-A		not specified	Uncertain significance (Oct 01, 2024)
12-111362899-G-A		not specified	Uncertain significance (Jun 09, 2022)
12-111362925-G-A		not specified	Uncertain significance (Apr 08, 2024)
12-111362956-G-A		not specified	Uncertain significance (Aug 19, 2024)
12-111362976-G-A		not specified	Uncertain significance (Nov 21, 2022)
12-111362995-A-G		not specified	Uncertain significance (Jan 17, 2025)
12-111363018-G-C		not specified	Uncertain significance (Mar 16, 2024)
12-111363123-T-C		not specified	Uncertain significance (Dec 07, 2021)
12-111363162-C-T		not specified	Uncertain significance (Jan 30, 2024)
12-111363163-G-A		not specified	Uncertain significance (Nov 12, 2024)
12-111363168-C-T		not specified	Uncertain significance (Jun 29, 2023)
12-111363177-G-A		not specified	Uncertain significance (Aug 27, 2024)
12-111363256-C-T		not specified	Uncertain significance (Mar 22, 2023)
12-111363264-C-T		not specified	Uncertain significance (Apr 24, 2024)
12-111363280-C-T		not specified	Uncertain significance (Feb 27, 2023)
12-111363292-G-A		not specified	Uncertain significance (Mar 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
PHETA1	protein_coding	protein_coding	ENST00000361483	2	8471

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0100	0.622	124865	0	15	124880	0.0000601

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.705	154	181	0.852	0.0000136	1627
Missense in Polyphen		52	68.391	0.76034		575
Synonymous	-0.0341	83	82.6	1.00	0.00000630	617
Loss of Function	0.357	3	3.75	0.801	1.59e-7	44

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000283	0.000273
Finnish	0.00	0.00
European (Non-Finnish)	0.0000180	0.0000178
Middle Eastern	0.000283	0.000273
South Asian	0.000103	0.0000980
Other	0.00	0.00

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}.

Haploinsufficiency Scores

• pHI: 0.139
• hipred: N
• hipred_score: 0.180
• ghis: 0.558

Essentials

• essential_gene_gene_trap: N

Mouse Genome Informatics

• Gene name: Pheta1

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