CD101

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

Basic information

Region (hg38): 1:117001749-117036552

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.

• Inborn genetic diseases (42 variants)
• not provided (13 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.

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				2	2	4
missense			40	3	7	50
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region				1		1
non coding						0
Total	0	0	40	5	9

Variants in CD101

This is a list of pathogenic ClinVar variants found in the CD101 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-117001825-G-A		not specified	Uncertain significance (Nov 15, 2021)
1-117009952-A-G		not specified	Uncertain significance (Dec 13, 2022)
1-117010068-C-T		not specified	Uncertain significance (Jan 24, 2024)
1-117010075-G-A		not specified	Likely benign (Jun 22, 2021)
1-117010116-G-A		not specified	Uncertain significance (Jul 12, 2023)
1-117010183-C-A		not specified	Uncertain significance (May 11, 2022)
1-117010186-A-G		not specified	Uncertain significance (Dec 19, 2023)
1-117011696-G-A		not specified	Uncertain significance (Oct 19, 2021)
1-117011711-A-G		not specified	Uncertain significance (Apr 13, 2022)
1-117011771-C-T		not specified	Uncertain significance (Dec 26, 2023)
1-117011799-A-G			Benign (Feb 23, 2021)
1-117011856-A-G		not specified	Uncertain significance (Mar 02, 2023)
1-117011864-C-A		not specified	Uncertain significance (Jan 20, 2023)
1-117011869-C-A		not specified	Uncertain significance (Dec 13, 2021)
1-117011913-T-A		not specified	Uncertain significance (Jan 17, 2024)
1-117011959-G-C		not specified	Uncertain significance (Dec 14, 2023)
1-117013503-A-G			Likely benign (May 08, 2018)
1-117013639-G-A		not specified	Uncertain significance (Apr 04, 2023)
1-117013649-T-C			Benign (May 16, 2018)
1-117013724-C-A		not specified	Uncertain significance (Oct 18, 2021)
1-117013754-A-G		not specified	Uncertain significance (Aug 16, 2022)
1-117017147-C-T		not specified	Uncertain significance (Apr 22, 2022)
1-117017258-A-T		not specified	Uncertain significance (Mar 15, 2023)
1-117017402-C-G		not specified	Uncertain significance (Jan 04, 2022)
1-117017413-C-T		not specified	Uncertain significance (Jul 27, 2022)

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
• 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