CD72

protein-coding

CD72 molecule, the group of CD molecules|C-type lectin domain containing

Gene summary

Enables receptor ligand activity and transmembrane signaling receptor activity. Involved in negative regulation of B cell receptor signaling pathway. Is active in plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001782.3

Inheritance

—

ClinVar variants

U:40B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.32

Max pathogenic AF

—

Genomic locus

chr9:35,609,982-35,646,810

External References & Databases

Ensembl (ENSG00000137101)

Transcript & Mutation Effects

hg38 • Region Span ~36.8 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 CD72 variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 40

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001782.3. 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						0
missense			38 clinvar	2 clinvar		40
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	40	2	0	42

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 13 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001782.3	RefSeq	NP_001773.1	8	MANE Select
ENST00000259633.9	Ensembl	ENSP00000259633.4	8	MANE Select
ENST00000378430.3	Ensembl	ENSP00000367687.3	3	Standard
ENST00000378430.4	Ensembl	ENSP00000367687.3	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

B cell receptor signaling pathway - Homo sapiens (human)
Developmental Biology
BCR
BCR signaling pathway
Other semaphorin interactions

Biological Process

cell adhesion

Molecular Function

transmembrane signaling receptor activity
signaling receptor binding
protein binding
carbohydrate binding

Cellular Component

plasma membrane
integral component of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000396757
Coding exons: 8
Length: 37278
Individuals with no LoFs: 125736
Homozygous LoFs: 0
Heterozygous LoFs: 12
Defined: 125748
p: 0.0000477

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.390	172	187	0.920	0.00000981	2289
Missense (PolyPhen)		29	41.422	0.70011		546
Synonymous	0.614	74	81.0	0.913	0.00000466	707
Loss of Function	2.97	7	22.0	0.317	0.00000103	251

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0	0.0	absent
European (Non-Finnish)	0.00011	0.000088	rare
South Asian	0	0.0	absent
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role in B-cell proliferation and differentiation.;

Recessive Scores

pRec: 0.0989

Intolerance Scores

LoFtool: 0.403
RVIS EVS: 0.37
RVIS percentile EVS: 75.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: N
Indispensability score: 0.0182

Gene Damage Prediction

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