CD164L2

CD164 molecule like 2

Basic information

Region (hg38): 1:27379175-27383333

Links

ENSG00000174950 ∙ NCBI:388611 ∙ ∙ HGNC:32043 ∙ Uniprot:Q6UWJ8 ∙ 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 CD164L2 gene.

• Inborn genetic diseases (6 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD164L2 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in CD164L2

This is a list of pathogenic ClinVar variants found in the CD164L2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-27380055-T-C		not specified	Uncertain significance (May 11, 2022)
1-27380130-C-T		not specified	Uncertain significance (Feb 10, 2022)
1-27381815-T-C		not specified	Uncertain significance (Feb 14, 2024)
1-27382506-C-T		not specified	Uncertain significance (Jul 16, 2021)
1-27382511-G-T		not specified	Uncertain significance (Oct 06, 2021)
1-27382586-A-C		not specified	Uncertain significance (Jun 28, 2022)
1-27382599-C-T		not specified	Uncertain significance (Mar 29, 2022)
1-27383165-C-A		not specified	Uncertain significance (Jan 10, 2023)
1-27383169-G-A		not specified	Uncertain significance (Nov 09, 2023)
1-27383181-A-G		not specified	Uncertain significance (Nov 03, 2023)
1-27383221-G-A		not specified	Uncertain significance (Oct 03, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD164L2	protein_coding	protein_coding	ENST00000374027	5	4205

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000115	0.378	125721	0	10	125731	0.0000398

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.204	101	107	0.944	0.00000632	1095
Missense in Polyphen		43	47.619	0.90301		521
Synonymous	1.31	33	44.1	0.749	0.00000262	351
Loss of Function	0.311	8	9.01	0.888	4.44e-7	101

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000178	0.0000176
Middle Eastern	0.0000544	0.0000544
South Asian	0.000100	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Intolerance Scores

• loftool: 0.728
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.32

Haploinsufficiency Scores

• pHI: 0.190
• hipred: N
• hipred_score: 0.144
• ghis: 0.486

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.171

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd164l2

Gene ontology

• Cellular component: integral component of membrane;cytoplasmic vesicle