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.

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.

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					2	2
missense			30		1	31
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	30	0	3

Variants in FCGRT

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

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

Position	Type	Phenotype	Significance	ClinVar
19-49513417-C-G		not specified	Uncertain significance (Feb 05, 2024)
19-49513452-C-T		not specified	Uncertain significance (Jan 07, 2022)
19-49513933-C-T		not specified	Uncertain significance (Dec 09, 2023)
19-49513934-G-T			Benign (Jul 06, 2018)
19-49513959-G-A		not specified	Uncertain significance (Jan 23, 2023)
19-49514001-C-G		not specified	Uncertain significance (Mar 04, 2024)
19-49514124-G-C		not specified	Uncertain significance (Mar 01, 2024)
19-49514217-A-G		not specified	Uncertain significance (Dec 26, 2023)
19-49514247-T-C		not specified	Uncertain significance (Dec 24, 2024)
19-49514252-C-T		not specified	Uncertain significance (Dec 03, 2024)
19-49514271-C-T		not specified	Uncertain significance (Nov 20, 2024)
19-49514281-G-C			Benign (Apr 25, 2018)
19-49514401-C-A		not specified	Uncertain significance (Jan 04, 2022)
19-49514433-C-G		not specified	Uncertain significance (May 09, 2023)
19-49514462-G-T		not specified	Uncertain significance (Feb 16, 2023)
19-49514474-C-A		not specified	Uncertain significance (Dec 03, 2021)
19-49524509-C-G		not specified	Uncertain significance (Feb 19, 2025)
19-49524513-C-A		not specified	Uncertain significance (May 03, 2023)
19-49524516-C-G		not specified	Uncertain significance (Jan 17, 2024)
19-49524632-G-A		not specified	Uncertain significance (Aug 12, 2024)
19-49524638-G-A		not specified	Uncertain significance (Feb 16, 2023)
19-49524653-G-A		not specified	Uncertain significance (Sep 01, 2021)
19-49524696-C-T		not specified	Uncertain significance (Nov 13, 2024)
19-49524715-G-C		not specified	Uncertain significance (Jun 03, 2022)
19-49524744-C-T		not specified	Uncertain significance (Jan 22, 2025)

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