CD163L1

protein-coding

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

Gene summary

This gene encodes a member of the scavenger receptor cysteine-rich (SRCR) superfamily. Members of this family are secreted or membrane-anchored proteins mainly found in cells associated with the immune system. The SRCR family is defined by a 100-110 amino acid SRCR domain, which may mediate protein-protein interaction and ligand binding. The encoded protein contains twelve SRCR domains, a transmembrane region and a cytoplasmic domain. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2014]

MANE transcript

NM_174941.6

Inheritance

—

ClinVar variants

U:171B:31

Top phenotype

EBV-positive nodal T- and NK-cell lymphoma

gnomAD constraint

pLI —, LoF o/e 0.68

Max pathogenic AF

—

Genomic locus

chr12:7,346,685-7,479,897

External References & Databases

Ensembl (ENSG00000177675)

Transcript & Mutation Effects

hg38 • Region Span ~133.2 kb

Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

schizophreniaNO_KNOWN

Inheritance Pattern: Unknown

Disease ID:MONDO:0005090

Submitter: Labcorp Genetics (formerly Invitae)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CD163L1 variants in ClinVar

3 Conditions Cataloged

not specifiedTotal: 176

not providedTotal: 14

EBV-positive nodal T- and NK-cell lymphomaTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_174941.6. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			2 clinvar	10 clinvar		12
missense			166 clinvar	20 clinvar	1 clinvar	187
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			3 clinvar			3
Total	0	0	171	30	1	202

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 22 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_174941.6	RefSeq	NP_777601.3	19	MANE Select
ENST00000313599.8	Ensembl	ENSP00000315945.3	19	MANE Select
NM_001297650.2	RefSeq	NP_001284579.2	19	Standard
ENST00000416109.2	Ensembl	ENSP00000393474.2	19	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

receptor-mediated endocytosis

Molecular Function

scavenger receptor activity

Cellular Component

extracellular region
external side of plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000313599
Coding exons: 19
Length: 133213
Individuals with no LoFs: 125236
Homozygous LoFs: 1
Heterozygous LoFs: 511
Defined: 125748
p: 0.00204

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	1.23	708	806	0.878	0.0000428	9493
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.0015	0.0015	notable
Latino/Admixed American	0.0018	0.0016	notable
Ashkenazi Jewish	0.0011	0.0011	notable
East Asian	0.0018	0.0018	notable
Finnish	0.00060	0.00060	rare
European (Non-Finnish)	0.0027	0.0026	notable
South Asian	0.0022	0.0022	notable
Other	0.0019	0.0015	notable

dbNSFP Gene Annotations

Source: dbNSFP

Recessive Scores

pRec: 0.0761

Intolerance Scores

LoFtool: 0.948
RVIS EVS: 0.4
RVIS percentile EVS: 76.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.136

Gene Damage Prediction

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