FCGR1A

protein-coding

Fc gamma receptor Ia, the group of CD molecules|Immunoglobulin like domain containing|Fc receptors

Gene summary

This gene encodes a protein that plays an important role in the immune response. This protein is a high-affinity Fc-gamma receptor. The gene is one of three related gene family members located on chromosome 1. [provided by RefSeq, Jul 2008]

MANE transcript

NM_000566.4

Inheritance

—

ClinVar variants

U:38B:8

Top phenotype

Peritoneal Gliomatosis

gnomAD constraint

pLI —, LoF o/e 0.6

Max pathogenic AF

—

Genomic locus

chr1:149,782,671-149,791,675

External References & Databases

Ensembl (ENSG00000150337)

Transcript & Mutation Effects

hg38 • Region Span ~9.0 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to FCGR1A variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 37

not providedTotal: 7

Peritoneal GliomatosisTotal: 1

FCGR1A-related disorderTotal: 1

IgG RECEPTOR I, PHAGOCYTIC, FAMILIAL DEFICIENCY OFTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_000566.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous				3 clinvar		3
missense			33 clinvar	5 clinvar		38
nonsense			2 clinvar			2
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	38	8	0	46

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 27 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_000566.4	RefSeq	NP_000557.1	6	MANE Select
ENST00000369168.5	Ensembl	ENSP00000358165.4	6	MANE Select
NM_001378804.1	RefSeq	NP_001365733.1	6	Standard
NM_001378805.1	RefSeq	NP_001365734.1	5	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Fc gamma R-mediated phagocytosis - Homo sapiens (human)
Systemic lupus erythematosus - Homo sapiens (human)
Acute myeloid leukemia - Homo sapiens (human)
Phagosome - Homo sapiens (human)
Staphylococcus aureus infection - Homo sapiens (human)

Biological Process

antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent
receptor-mediated endocytosis
phagocytosis, engulfment
immune response
signal transduction

Molecular Function

protein binding
IgG binding

Cellular Component

plasma membrane
integral component of membrane
clathrin-coated endocytic vesicle membrane
early endosome membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000369168
Coding exons: 6
Length: 9848
Individuals with no LoFs: 123711
Homozygous LoFs: 6
Heterozygous LoFs: 1042
Defined: 124759
p: 0.00421

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.579	150	171	0.875	0.00000860	2410
Missense (PolyPhen)		26	46.8	0.55555		721
Synonymous	0.372	63	66.9	0.942	0.00000327	739
Loss of Function	1.35	8	13.3	0.600	7.18e-7	160

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0013	0.0011	notable
Latino/Admixed American	0.0031	0.0031	notable
Ashkenazi Jewish	0.00030	0.00030	rare
East Asian	0.00017	0.00016	rare
Finnish	0.00051	0.00051	rare
European (Non-Finnish)	0.0064	0.0063	notable
South Asian	0.0059	0.0057	notable
Other	0.0046	0.0044	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: High affinity receptor for the Fc region of immunoglobulins gamma. Functions in both innate and adaptive immune responses. {ECO:0000269|PubMed:10397749, ECO:0000269|PubMed:10514529, ECO:0000269|PubMed:21965667, ECO:0000269|PubMed:8611682, ECO:0000269|PubMed:9881690}.;

Recessive Scores

pRec: 0.265

Essentials

Essential (CRISPR): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.308

Gene Damage Prediction

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