CD248

protein-coding

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

Gene summary

Predicted to enable extracellular matrix binding activity and extracellular matrix protein binding activity. Predicted to be involved in cell migration. Predicted to act upstream of or within several processes, including anatomical structure regression; lymph node development; and positive regulation of endothelial cell apoptotic process. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

CD164L1

MANE transcript

NM_020404.3

Inheritance

—

ClinVar variants

U:102B:21

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.29

Max pathogenic AF

—

Genomic locus

chr11:66,314,494-66,317,044

External References & Databases

Ensembl (ENSG00000174807)

Transcript & Mutation Effects

hg38 • Region Span ~2.6 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 CD248 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 110

not providedTotal: 13

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_020404.3. 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				1 clinvar	10 clinvar	11
missense			102 clinvar	9 clinvar	1 clinvar	112
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	102	10	11	123

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 2 of 2 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_020404.3	RefSeq	NP_065137.1	1	MANE Select
ENST00000311330.4	Ensembl	ENSP00000308117.3	1	MANE Select

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

biological_process
positive regulation of cell population proliferation
cell migration
lymph node development
anatomical structure regression

Molecular Function

molecular_function
calcium ion binding
carbohydrate binding
extracellular matrix binding
extracellular matrix protein binding

Cellular Component

cytoplasm
external side of plasma membrane
integral component of membrane
extracellular matrix
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000311330
Coding exons: 1
Length: 2558
Individuals with no LoFs: 0
Homozygous LoFs: 0
Heterozygous LoFs: 0
Defined: 0
p: 0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.21	388	461	0.841	0.0000286	4789
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0	0.0	absent
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

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

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.109

Gene Damage Prediction

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