CD7

CD7 molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 17:82313564-82317608

Links

ENSG00000173762 ∙ NCBI:924 ∙ OMIM:186820 ∙ HGNC:1695 ∙ Uniprot:P09564 ∙ 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 CD7 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD7 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						0
missense			13	3		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			1			1
Total	0	0	14	3	0

Variants in CD7

This is a list of pathogenic ClinVar variants found in the CD7 region.

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

Position	Type	Phenotype	Significance	ClinVar
17-82315359-G-T		not specified	Uncertain significance (Oct 13, 2023)
17-82315400-T-C		not specified	Likely benign (Feb 23, 2023)
17-82315409-C-T		not specified	Uncertain significance (Oct 12, 2022)
17-82315426-C-G		not specified	Uncertain significance (Oct 02, 2023)
17-82316230-C-T		not specified	Uncertain significance (Jun 21, 2023)
17-82316331-G-A		not specified	Uncertain significance (May 09, 2023)
17-82316343-G-A		not specified	Uncertain significance (Dec 19, 2023)
17-82316347-C-T		not specified	Uncertain significance (Mar 20, 2024)
17-82316694-C-T		not specified	Uncertain significance (Nov 08, 2022)
17-82316735-C-T		not specified	Uncertain significance (Apr 10, 2023)
17-82316756-C-T		not specified	Likely benign (Jun 05, 2023)
17-82316783-T-C		not specified	Uncertain significance (Jun 23, 2023)
17-82316804-C-T		not specified	Uncertain significance (Mar 28, 2023)
17-82316821-G-T		not specified	Uncertain significance (Feb 10, 2022)
17-82316928-T-C		not specified	Uncertain significance (Feb 03, 2022)
17-82317440-C-A		not specified	Uncertain significance (May 31, 2023)
17-82317482-G-A		not specified	Uncertain significance (Oct 14, 2021)
17-82317486-G-C		not specified	Likely benign (Apr 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD7	protein_coding	protein_coding	ENST00000312648	4	2735

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0513	0.869	125669	0	3	125672	0.0000119

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.540	133	152	0.877	0.00000972	1472
Missense in Polyphen		34	38.864	0.87485		417
Synonymous	0.0769	76	76.9	0.989	0.00000542	558
Loss of Function	1.45	3	7.22	0.416	3.09e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000620	0.0000615
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000885	0.00000880
Middle Eastern	0.0000545	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Not yet known.
• Pathway: Hematopoietic cell lineage - Homo sapiens (human);TCR (Consensus)

Intolerance Scores

• loftool: 0.394
• rvis_EVS: 0.55
• rvis_percentile_EVS: 81.48

Haploinsufficiency Scores

• pHI: 0.117
• hipred: N
• hipred_score: 0.340
• ghis: 0.394

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0689

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd7
• Phenotype: endocrine/exocrine gland phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: adaptive immune response;immune response;transmembrane receptor protein tyrosine kinase signaling pathway;T cell activation
• Cellular component: plasma membrane;membrane;integral component of membrane
• Molecular function: signaling receptor activity