CD248

CD248 molecule, the group of CD molecules|C-type lectin domain containing

Basic information

Region (hg38): 11:66314493-66317044

Previous symbols: [ "CD164L1" ]

Links

ENSG00000174807 ∙ NCBI:57124 ∙ OMIM:606064 ∙ HGNC:18219 ∙ Uniprot:Q9HCU0 ∙ 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 CD248 gene.

• Inborn genetic diseases (28 variants)
• not provided (13 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD248 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					10	10
missense			26	4	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	26	4	11

Variants in CD248

This is a list of pathogenic ClinVar variants found in the CD248 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-66314801-G-A		not specified	Uncertain significance (Dec 14, 2023)
11-66314866-C-T		not specified	Uncertain significance (Apr 28, 2022)
11-66314880-A-C		not specified	Uncertain significance (Dec 19, 2022)
11-66314887-C-T		not specified	Uncertain significance (Dec 20, 2023)
11-66314894-G-A		not specified	Uncertain significance (Jan 10, 2022)
11-66314948-G-T		not specified	Uncertain significance (Feb 23, 2023)
11-66314986-T-C		not specified	Likely benign (Jan 30, 2024)
11-66314997-G-A			Benign (Jan 30, 2018)
11-66315008-C-G		not specified	Uncertain significance (Mar 02, 2023)
11-66315062-C-T		not specified	Uncertain significance (Jun 21, 2022)
11-66315067-T-G		not specified	Uncertain significance (Jan 16, 2024)
11-66315188-G-T		not specified	Uncertain significance (Oct 05, 2023)
11-66315234-G-A			Benign (Apr 10, 2018)
11-66315269-T-G			Likely benign (Jul 13, 2018)
11-66315278-T-C		not specified	Uncertain significance (Jun 22, 2023)
11-66315319-G-A		not specified	Uncertain significance (Mar 02, 2023)
11-66315321-G-C			Benign (Feb 26, 2018)
11-66315323-C-T		not specified	Likely benign (Jun 13, 2022)
11-66315391-T-C		not specified	Uncertain significance (Jan 24, 2023)
11-66315419-G-A		not specified	Uncertain significance (Sep 20, 2023)
11-66315433-A-T		not specified	Uncertain significance (Jan 18, 2023)
11-66315554-G-C		not specified	Uncertain significance (Sep 20, 2023)
11-66315572-C-T			Benign (Apr 10, 2018)
11-66315573-G-A			Benign (Feb 01, 2018)
11-66315636-G-C		not specified	Uncertain significance (Jan 23, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD248	protein_coding	protein_coding	ENST00000311330	1	2558

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0590	0.940	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.21	388	461	0.841	0.0000286	4789
Missense in Polyphen		134	173.18	0.77375		1803
Synonymous	0.465	198	206	0.959	0.0000140	1691
Loss of Function	2.98	6	20.6	0.291	8.97e-7	206

LoF frequencies by population

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

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in tumor angiogenesis. {ECO:0000269|PubMed:15862292}.

Recessive Scores

• pRec: 0.129

Intolerance Scores

• loftool: 0.0610
• rvis_EVS: 0.32
• rvis_percentile_EVS: 72.81

Haploinsufficiency Scores

• pHI: 0.222
• hipred: Y
• hipred_score: 0.527
• ghis: 0.466

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.109

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd248
• Phenotype: normal phenotype; neoplasm

Gene ontology

• Biological process: biological_process;positive regulation of cell population proliferation;cell migration;lymph node development;anatomical structure regression;positive regulation of endothelial cell apoptotic process
• Cellular component: cytoplasm;external side of plasma membrane;integral component of membrane;extracellular matrix;extracellular exosome
• Molecular function: molecular_function;calcium ion binding;carbohydrate binding;extracellular matrix binding;extracellular matrix protein binding