CD163L1

CD163 molecule like 1, the group of Scavenger receptor cysteine rich domain containing|Scavenger receptors

Basic information

Region (hg38): 12:7346685-7479897

Links

ENSG00000177675 ∙ NCBI:283316 ∙ OMIM:606079 ∙ HGNC:30375 ∙ Uniprot:Q9NR16 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• schizophrenia (No Known Disease Relationship), mode of inheritance: Unknown

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CD163L1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD163L1 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				10		10
missense			64	11	1	76
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	64	21	1

Variants in CD163L1

This is a list of pathogenic ClinVar variants found in the CD163L1 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7357451-C-T		not specified	Uncertain significance (Mar 29, 2022)
12-7367239-A-G		not specified	Uncertain significance (Oct 26, 2022)
12-7367263-C-G		not specified	Uncertain significance (Jul 26, 2023)
12-7368939-A-G			Likely benign (Feb 01, 2024)
12-7368945-T-C		not specified	Uncertain significance (Jan 02, 2024)
12-7369385-G-C		not specified	Uncertain significance (Mar 01, 2024)
12-7369417-C-T		not specified	Uncertain significance (Oct 30, 2023)
12-7369456-G-A		not specified	Uncertain significance (Jan 04, 2024)
12-7369575-G-T			Benign (May 16, 2018)
12-7369593-C-T		not specified	Uncertain significance (Mar 29, 2022)
12-7369606-C-A		not specified	Uncertain significance (Dec 01, 2022)
12-7369636-C-T		not specified	Uncertain significance (Aug 29, 2023)
12-7369645-C-T		not specified	Uncertain significance (Nov 10, 2024)
12-7373393-T-C		not specified	Uncertain significance (Jul 14, 2022)
12-7373400-A-C		not specified	Uncertain significance (Apr 06, 2022)
12-7373406-G-A		not specified	Uncertain significance (Jun 21, 2023)
12-7373467-C-T		not specified	Uncertain significance (Jan 26, 2022)
12-7373524-T-C		not specified	Uncertain significance (Jun 07, 2023)
12-7373526-G-A		not specified	Uncertain significance (Sep 14, 2023)
12-7373530-T-C		not specified	Likely benign (Aug 05, 2024)
12-7373551-C-T		not specified	Uncertain significance (May 26, 2024)
12-7374458-T-C			Likely benign (Nov 01, 2022)
12-7374458-T-G			Likely benign (Nov 01, 2022)
12-7374473-C-T			Likely benign (Apr 01, 2024)
12-7374497-G-C			Likely benign (Apr 01, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD163L1	protein_coding	protein_coding	ENST00000313599	19	133213

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.79e-26	0.828	125236	1	511	125748	0.00204

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.23	708	806	0.878	0.0000428	9493
Missense in Polyphen		258	320.44	0.80515		3923
Synonymous	1.96	267	311	0.859	0.0000182	2803
Loss of Function	2.55	52	76.0	0.685	0.00000407	837

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00331	0.00331
Ashkenazi Jewish	0.00109	0.00109
East Asian	0.00181	0.00180
Finnish	0.000603	0.000601
European (Non-Finnish)	0.00267	0.00263
Middle Eastern	0.00181	0.00180
South Asian	0.00223	0.00219
Other	0.00189	0.00147

dbNSFP

Source: dbNSFP

Recessive Scores

• pRec: 0.0761

Intolerance Scores

• loftool: 0.948
• rvis_EVS: 0.4
• rvis_percentile_EVS: 76.16

Haploinsufficiency Scores

• pHI: 0.0527
• hipred: N
• hipred_score: 0.163
• ghis: 0.373

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.136

Gene Damage Prediction

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

Gene ontology

• Biological process: receptor-mediated endocytosis
• Cellular component: extracellular region;external side of plasma membrane;integral component of membrane
• Molecular function: scavenger receptor activity