CD101

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

Basic information

Region (hg38): 1:117001750-117036552

Previous symbols: [ "IGSF2" ]

Links

ENSG00000134256

∙ NCBI:9398 ∙ OMIM:604516 ∙ HGNC:5949 ∙ Uniprot:Q93033 ∙ 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 CD101 gene.

not_specified (117 variants)
not_provided (11 variants)
CD101-related_disorder (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD101 gene is commonly pathogenic or not. These statistics are base on transcript: NM_001256106.3. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				4 clinvar	2 clinvar	6
missense			108 clinvar	10 clinvar	5 clinvar	123
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	110	14	7

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD101	protein_coding	protein_coding	ENST00000256652	9	34786

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.28e-13	0.972	125450	0	298	125748	0.00119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.360	528	552	0.957	0.0000291	6644
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00239	0.00239
Ashkenazi Jewish	0.00	0.00
East Asian	0.00131	0.00131
Finnish	0.00342	0.00342
European (Non-Finnish)	0.000936	0.000932
Middle Eastern	0.00131	0.00131
South Asian	0.000392	0.000392
Other	0.00228	0.00228

dbNSFP

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}.;
Pathway: Generation of second messenger molecules;TCR signaling;Immune System;Adaptive Immune System (Consensus)

Recessive Scores

pRec: 0.162

Intolerance Scores

loftool: 0.624
rvis_EVS: 1.68
rvis_percentile_EVS: 96.34

Haploinsufficiency Scores

pHI: 0.128
hipred: N
hipred_score: 0.123
ghis: 0.392

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: E
gene_indispensability_score: 0.539

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Cd101
Phenotype: immune system phenotype; hematopoietic system phenotype;

Gene ontology

Biological process: positive regulation of myeloid leukocyte differentiation;cell surface receptor signaling pathway
Cellular component: plasma membrane;integral component of membrane;extracellular exosome
Molecular function: hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides