AMER3

APC membrane recruitment protein 3, the group of APC membrane recruitment proteins

Basic information

Region (hg38): 2:130755540-130768134

Previous symbols: [ "FAM123C" ]

Links

ENSG00000178171 ∙ NCBI:205147 ∙ ∙ HGNC:26771 ∙ Uniprot:Q8N944 ∙ 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 AMER3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the AMER3 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			93	10		103
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	93	10	0

Variants in AMER3

This is a list of pathogenic ClinVar variants found in the AMER3 region.

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

Position	Type	Phenotype	Significance	ClinVar
2-130762086-G-C		not specified	Uncertain significance (May 15, 2025)
2-130762141-C-G		not specified	Uncertain significance (Jan 31, 2023)
2-130762145-G-A		not specified	Uncertain significance (Aug 01, 2024)
2-130762193-C-G		not specified	Uncertain significance (Jan 06, 2023)
2-130762199-G-A		not specified	Uncertain significance (Feb 09, 2025)
2-130762211-C-T		not specified	Uncertain significance (Aug 14, 2024)
2-130762220-G-A		not specified	Uncertain significance (Apr 20, 2023)
2-130762227-G-A		not specified	Likely benign (Jan 09, 2025)
2-130762235-G-A		not specified	Uncertain significance (Mar 07, 2025)
2-130762280-G-A		not specified	Uncertain significance (Mar 17, 2025)
2-130762298-G-A		not specified	Uncertain significance (Mar 08, 2025)
2-130762341-G-A		not specified	Uncertain significance (Dec 18, 2023)
2-130762368-C-T		not specified	Uncertain significance (Aug 01, 2022)
2-130762371-G-C		not specified	Uncertain significance (Mar 11, 2022)
2-130762398-G-A		not specified	Uncertain significance (Mar 20, 2024)
2-130762442-C-T		not specified	Uncertain significance (Apr 26, 2023)
2-130762445-C-T		not specified	Uncertain significance (Aug 02, 2021)
2-130762460-C-T		not specified	Uncertain significance (Aug 22, 2023)
2-130762461-G-A		not specified	Uncertain significance (Jul 11, 2023)
2-130762472-C-G		not specified	Uncertain significance (May 18, 2025)
2-130762479-T-C		not specified	Uncertain significance (May 08, 2024)
2-130762483-C-T		EBV-positive nodal T- and NK-cell lymphoma	Likely benign (-)
2-130762503-A-G		not specified	Uncertain significance (Jun 11, 2025)
2-130762508-A-G		not specified	Uncertain significance (Feb 22, 2025)
2-130762533-A-G		not specified	Uncertain significance (Apr 10, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
AMER3	protein_coding	protein_coding	ENST00000423981	1	12700

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.619	0.380	125724	0	8	125732	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.671	561	518	1.08	0.0000315	5473
Missense in Polyphen		129	149.25	0.86431		1689
Synonymous	-1.74	265	231	1.15	0.0000153	1894
Loss of Function	2.62	2	11.7	0.171	6.59e-7	126

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000103	0.0000905
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000550	0.0000544
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.00000889	0.00000879
Middle Eastern	0.0000550	0.0000544
South Asian	0.0000327	0.0000327
Other	0.000333	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Regulator of the canonical Wnt signaling pathway. Acts by specifically binding phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), translocating to the cell membrane (By similarity). {ECO:0000250}.

Intolerance Scores

• rvis_EVS: -1.08
• rvis_percentile_EVS: 7.24

Haploinsufficiency Scores

• pHI: 0.137
• hipred: N
• hipred_score: 0.246
• ghis: 0.659

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Amer3

Gene ontology

• Biological process: Wnt signaling pathway;regulation of canonical Wnt signaling pathway
• Cellular component: plasma membrane
• Molecular function: protein binding;phosphatidylinositol-4,5-bisphosphate binding;beta-catenin binding