FCGRT

Fc gamma receptor and transporter, the group of C1-set domain containing

Basic information

Region (hg38): 19:49506816-49526428

Links

ENSG00000104870

∙ NCBI:2217 ∙ OMIM:601437 ∙ HGNC:3621 ∙ Uniprot:P55899 ∙ 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 FCGRT gene.

not_specified (46 variants)
not_provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCGRT gene is commonly pathogenic or not. These statistics are base on transcript: NM_001136019.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous					2 clinvar	2
missense			45 clinvar	1 clinvar	1 clinvar	47
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	1	3

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
FCGRT	protein_coding	protein_coding	ENST00000221466	6	19518

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0415	0.953	125740	0	8	125748	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.843	176	210	0.836	0.0000131	2305
Missense in Polyphen		60	87.73	0.68391		937
Synonymous	-0.237	105	102	1.03	0.00000746	786
Loss of Function	2.43	5	15.2	0.329	7.38e-7	162

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000290	0.0000290
Ashkenazi Jewish	0.000100	0.0000992
East Asian	0.000164	0.000163
Finnish	0.0000465	0.0000462
European (Non-Finnish)	0.0000180	0.0000176
Middle Eastern	0.000164	0.000163
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Binds to the Fc region of monomeric immunoglobulins gamma (PubMed:7964511, PubMed:10933786). Mediates the selective uptake of IgG from milk and helps newborn animals to acquire passive immunity. IgG in the milk is bound at the apical surface of the intestinal epithelium. The resultant FcRn-IgG complexes are transcytosed across the intestinal epithelium and IgG is released from FcRn into blood or tissue fluids (By similarity). Possible role in transfer of immunoglobulin G from mother to fetus (PubMed:7964511). {ECO:0000250|UniProtKB:P13599, ECO:0000269|PubMed:10933786, ECO:0000269|PubMed:7964511}.;

Recessive Scores

pRec: 0.415

Intolerance Scores

loftool: 0.0854
rvis_EVS: -0.14
rvis_percentile_EVS: 43.57

Haploinsufficiency Scores

pHI: 0.396
hipred: N
hipred_score: 0.419
ghis: 0.546

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: E
gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Fcgrt
Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);

Gene ontology

Biological process: IgG immunoglobulin transcytosis in epithelial cells mediated by FcRn immunoglobulin receptor;immune response
Cellular component: extracellular space;plasma membrane;external side of plasma membrane;integral component of membrane
Molecular function: IgG binding;beta-2-microglobulin binding;peptide antigen binding