CD244

CD244 molecule, the group of CD molecules|Ig-like cell adhesion molecule family|Immunoglobulin like domain containing

Basic information

Region (hg38): 1:160830159-160862887

Links

ENSG00000122223 ∙ NCBI:51744 ∙ OMIM:605554 ∙ HGNC:18171 ∙ Uniprot:Q9BZW8 ∙ 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 CD244 gene.

• Inborn genetic diseases (15 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD244 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					1	1
missense			10	5	1	16
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	10	5	3

Variants in CD244

This is a list of pathogenic ClinVar variants found in the CD244 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160830769-A-G			Benign (Oct 28, 2020)
1-160831365-G-T		not specified	Uncertain significance (Jul 21, 2022)
1-160831381-C-T		not specified	Uncertain significance (Dec 18, 2023)
1-160831382-G-A		CD244-related disorder	Benign (Apr 08, 2019)
1-160832565-C-T		Malignant tumor of prostate	Uncertain significance (-)
1-160832568-G-T		not specified	Uncertain significance (Jan 23, 2023)
1-160834107-G-T		not specified	Uncertain significance (Aug 22, 2023)
1-160837925-T-C		Rheumatoid arthritis	risk factor (Oct 01, 2008)
1-160838492-T-C		not specified	Likely benign (Feb 06, 2023)
1-160838998-A-G		not specified	Uncertain significance (May 04, 2022)
1-160839020-T-C			Benign (Jun 29, 2018)
1-160841211-C-A		not specified	Likely benign (Oct 03, 2022)
1-160841214-A-C		not specified	Uncertain significance (Aug 12, 2021)
1-160841248-G-T		not specified	Uncertain significance (Nov 02, 2023)
1-160841254-C-T		not specified	Likely benign (Jun 02, 2023)
1-160841330-A-G		not specified	Likely benign (Aug 16, 2022)
1-160841448-C-A		not specified	Uncertain significance (Nov 10, 2022)
1-160841468-G-A		not specified	Uncertain significance (Mar 07, 2024)
1-160841488-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-160841489-G-A		not specified	Uncertain significance (Nov 03, 2022)
1-160841715-A-T		not specified	Uncertain significance (Jun 23, 2021)
1-160841740-G-T		not specified	Likely benign (Nov 16, 2021)
1-160841831-T-C		not specified	Uncertain significance (Oct 26, 2021)
1-160862639-G-A		CD244-related disorder	Benign (Dec 23, 2019)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD244	protein_coding	protein_coding	ENST00000368033	9	32743

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0573	0.942	125738	0	8	125746	0.0000318

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.301	179	191	0.939	0.00000929	2423
Missense in Polyphen		32	49.909	0.64117		666
Synonymous	-0.431	81	76.2	1.06	0.00000404	700
Loss of Function	2.97	6	20.5	0.292	9.74e-7	233

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.000298	0.000298
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000177	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Heterophilic receptor of the signaling lymphocytic activation molecule (SLAM) family; its ligand is CD48. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. Acts as activating natural killer (NK) cell receptor (PubMed:10359122, PubMed:8376943, PubMed:11714776). Activating function implicates association with SH2D1A and FYN (PubMed:15713798). Downstreaming signaling involves predominantly VAV1, and, to a lesser degree, INPP5D/SHIP1 and CBL. Signal attenuation in the absence of SH2D1A is proposed to be dependent on INPP5D and to a lesser extent PTPN6/SHP-1 and PTPN11/SHP-2 (PubMed:10934222, PubMed:15713798). Stimulates NK cell cytotoxicity, production of IFN-gamma and granule exocytosis (PubMed:8376943, PubMed:11714776). Optimal expansion and activation of NK cells seems to be dependent on the engagement of CD244 with CD48 expressed on neighboring NK cells (By similarity). Acts as costimulator in NK activation by enhancing signals by other NK receptors such as NCR3 and NCR1 (PubMed:10741393). At early stages of NK cell differentiation may function as an inhibitory receptor possibly ensuring the self- tolerance of developing NK cells (PubMed:11917118). Involved in the regulation of CD8(+) T-cell proliferation; expression on activated T-cells and binding to CD488 provides costimulatory-like function for neighboring T-cells (By similarity). Inhibits inflammatory responses in dendritic cells (DCs) (By similarity). {ECO:0000250|UniProtKB:Q07763, ECO:0000269|PubMed:10359122, ECO:0000269|PubMed:10741393, ECO:0000269|PubMed:10934222, ECO:0000269|PubMed:11714776, ECO:0000269|PubMed:11917118, ECO:0000269|PubMed:8376943, ECO:0000305|PubMed:15713798}.
• Pathway: Natural killer cell mediated cytotoxicity - Homo sapiens (human);Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.275

Intolerance Scores

• loftool: 0.727
• rvis_EVS: 0.37
• rvis_percentile_EVS: 75.43

Haploinsufficiency Scores

• pHI: 0.0307
• hipred: N
• hipred_score: 0.212
• ghis: 0.421

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.000358

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd244a
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: adaptive immune response;natural killer cell activation involved in immune response;signal transduction;innate immune response;leukocyte migration;positive regulation of inositol phosphate biosynthetic process;positive regulation of granzyme B production;positive regulation of interferon-gamma secretion;positive regulation of interleukin-8 secretion
• Cellular component: plasma membrane;external side of plasma membrane;integral component of membrane
• Molecular function: protein binding;signaling receptor activity;MHC class I protein binding