CD101

protein-coding

CD101 molecule, the group of I-set domain containing|V-set domain containing|CD molecules

Gene summary

Predicted to enable hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides. Predicted to be involved in cell surface receptor signaling pathway. Predicted to act upstream of or within several processes, including T cell homeostasis; positive regulation of myeloid leukocyte differentiation; and response to insulin. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jun 2026]

Previous symbols:

IGSF2

MANE transcript

NM_001256106.3

Inheritance

—

ClinVar variants

U:127B:22

Top phenotype

CD101-related disorder

gnomAD constraint

pLI —, LoF o/e 0.62

Max pathogenic AF

—

Genomic locus

chr1:117,001,750-117,036,552

External References & Databases

Ensembl (ENSG00000134256)

Transcript & Mutation Effects

hg38 • Region Span ~34.8 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 CD101 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 128

not providedTotal: 13

CD101-related disorderTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001256106.3. 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			2 clinvar	4 clinvar	2 clinvar	8
missense			121 clinvar	11 clinvar	5 clinvar	137
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	127	15	7	149

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 21 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001256106.3	RefSeq	NP_001243035.1	9	MANE Select
ENST00000682167.1	Ensembl	ENSP00000508039.1	9	MANE Select
NM_001256109.3	RefSeq	NP_001243038.1	9	Standard
NM_001256111.3	RefSeq	NP_001243040.1	9	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Generation of second messenger molecules
TCR signaling
Immune System
Adaptive Immune System

Biological Process

positive regulation of myeloid leukocyte differentiation
cell surface receptor signaling pathway

Molecular Function

hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides

Cellular Component

plasma membrane
integral component of membrane
extracellular exosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000256652
Coding exons: 9
Length: 34786
Individuals with no LoFs: 125450
Homozygous LoFs: 0
Heterozygous LoFs: 298
Defined: 125748
p: 0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.360	528	552	0.957	0.0000291	6644
Missense (PolyPhen)		117	131.43	0.89022		1657
Synonymous	0.292	217	223	0.975	0.0000124	2022
Loss of Function	2.35	27	43.8	0.616	0.00000202	518

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00080	0.00080	rare
Latino/Admixed American	0.0016	0.0016	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.0013	0.0013	notable
Finnish	0.0034	0.0034	notable
European (Non-Finnish)	0.00094	0.00093	rare
South Asian	0.00039	0.00039	rare
Other	0.0023	0.0023	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Plays a role as inhibitor of T-cells proliferation induced by CD3. Inhibits expression of IL2RA on activated T-cells and secretion of IL2. Inhibits tyrosine kinases that are required for IL2 production and cellular proliferation. Inhibits phospholipase C-gamma-1/PLCG1 phosphorylation and subsequent CD3- induced changes in intracellular free calcium. Prevents nuclear translocation of nuclear factor of activated T-cell to the nucleus. Plays a role in the inhibition of T-cell proliferation via IL10 secretion by cutaneous dendritic cells. May be a marker of CD4(+) CD56(+) leukemic tumor cells. {ECO:0000269|PubMed:11093127, ECO:0000269|PubMed:15737213, ECO:0000269|PubMed:7722299, ECO:0000269|PubMed:9233604, ECO:0000269|PubMed:9389317, ECO:0000269|PubMed:9647226}.;

Recessive Scores

pRec: 0.162

Intolerance Scores

LoFtool: 0.624
RVIS EVS: 1.68
RVIS percentile EVS: 96.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Indispensability pred.: E
Indispensability score: 0.539

Gene Damage Prediction

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