SIGLECL1

Summary

SIGLECL1 (SIGLEC family like 1, HGNC:26856) is a protein-coding gene on chromosome 19q13.41, encoding SIGLEC family-like protein 1 (Q8N7X8).

Predicted to be located in membrane.

Source: NCBI Gene 284369 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 27 total
• MANE Select transcript: NM_001385465

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26856
Approved symbol	SIGLECL1
Name	SIGLEC family like 1
Location	19q13.41
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40235
Ensembl gene	ENSG00000179213
Ensembl biotype	protein_coding
Entrez	284369

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000316401, ENST00000593968, ENST00000596117, ENST00000597610, ENST00000597824, ENST00000599553, ENST00000601727, ENST00000614422

RefSeq mRNA: 5 — MANE Select: NM_001385465 NM_001308437, NM_001385465, NM_001385466, NM_001385467, NM_173635

CCDS: CCDS12827, CCDS77341

Canonical transcript exons

ENST00000601727 — 6 exons

Exon	Start	End
ENSE00001255523	51265368	51265649
ENSE00001364686	51268571	51269330
ENSE00001417315	51263883	51264094
ENSE00003477975	51265777	51265882
ENSE00003676559	51267373	51267529
ENSE00003930789	51251080	51251545

Expression profiles

Bgee: expression breadth broad, 53 present calls, max score 93.93.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0601 / max 36.0868, expressed in 10 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
177207	0.0349	4
177208	0.0167	8
177209	0.0086	3

Top tissues by expression

175 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	93.93	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.91	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	86.17	gold quality
left testis	UBERON:0004533	84.65	gold quality
right testis	UBERON:0004534	82.91	gold quality
testis	UBERON:0000473	82.61	gold quality
adult organism	UBERON:0007023	80.24	gold quality
monocyte	CL:0000576	51.39	gold quality
leukocyte	CL:0000738	50.03	gold quality
sural nerve	UBERON:0015488	48.62	silver quality
upper leg skin	UBERON:0004262	43.50	silver quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
granulocyte	CL:0000094	42.98	silver quality
secondary oocyte	CL:0000655	42.57	gold quality
cortical plate	UBERON:0005343	41.77	gold quality
epithelium of nasopharynx	UBERON:0001951	41.70	gold quality
spleen	UBERON:0002106	41.56	silver quality
vastus lateralis	UBERON:0001379	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
blood	UBERON:0000178	41.34	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of stomach	UBERON:0001199	41.04	silver quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality
myocardium	UBERON:0002349	40.45	gold quality
gingival epithelium	UBERON:0001949	40.43	gold quality
germinal epithelium of ovary	UBERON:0001304	40.33	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.28

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

29 targeting SIGLECL1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-4658	99.77	64.94	514
HSA-MIR-6790-5P	99.77	65.24	505
HSA-MIR-4679	99.76	69.19	1229
HSA-MIR-3659	99.70	67.97	694
HSA-MIR-4516	99.61	67.78	3390
HSA-MIR-4677-3P	99.49	67.91	1246
HSA-MIR-488-5P	99.28	68.12	821
HSA-MIR-4685-5P	99.25	65.99	1563
HSA-MIR-6837-5P	99.25	65.47	1632
HSA-MIR-8065	99.19	70.38	1289
HSA-MIR-155-3P	99.03	67.99	924
HSA-MIR-5701	98.97	69.54	1502
HSA-MIR-6868-3P	98.63	69.64	2259
HSA-MIR-6776-5P	98.54	67.43	1304
HSA-MIR-4662A-5P	98.48	67.18	1007
HSA-MIR-138-5P	98.43	70.49	1292
HSA-MIR-7113-5P	97.88	67.33	1735
HSA-MIR-1279	97.83	67.50	1898
HSA-MIR-4475	97.36	66.95	761
HSA-MIR-6892-5P	97.27	68.60	847
HSA-MIR-7161-3P	96.79	68.79	798
HSA-MIR-3655	86.11	61.77	117

Literature-anchored findings (GeneRIF, showing 1)

• CD33 and SIGLECL1 Immunoglobulin Superfamily Involved in Dementia. (PMID:32647856)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Siglecl1	ENSMUSG00000108695
rattus_norvegicus	Siglecl1	ENSRNOG00000059992

Paralogs (16): CD22 (ENSG00000012124), SIGLEC1 (ENSG00000088827), SIGLEC8 (ENSG00000105366), CD33 (ENSG00000105383), SIGLEC6 (ENSG00000105492), MAG (ENSG00000105695), SIGLEC9 (ENSG00000129450), SIGLEC10 (ENSG00000142512), TMEM25 (ENSG00000149582), SIGLEC11 (ENSG00000161640), SIGLEC16 (ENSG00000161643), SIGLEC7 (ENSG00000168995), SIGLEC15 (ENSG00000197046), SIGLEC14 (ENSG00000254415), SIGLEC12 (ENSG00000254521), SIGLEC5 (ENSG00000268500)

Protein

Protein identifiers

SIGLEC family-like protein 1 — Q8N7X8 (reviewed: Q8N7X8)

All UniProt accessions (5): B7ZLS6, Q8N7X8, M0QY48, M0QY54, M0R2N8

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (5): NP_001295366, NP_001372394, NP_001372395, NP_001372396, NP_775906 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR013783	Ig-like_fold	Homologous_superfamily
IPR036179	Ig-like_dom_sf	Homologous_superfamily
IPR051036	SIGLEC	Family

UniProt features (4 total): chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N7X8-F1	82.98	0.61

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 15 (showing top): E2F5_TARGET_GENES, MAFG_TARGET_GENES, ZNF274_TARGET_GENES, MIR8065, MIR138_5P, MIR7113_5P, MIR3659, GSE13485_DAY1_VS_DAY3_YF17D_VACCINE_PBMC_UP, GSE13485_DAY1_VS_DAY7_YF17D_VACCINE_PBMC_UP, GSE15659_NAIVE_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_CD45RA_NEG_CD4_TCELL_VS_NONSUPPRESSIVE_TCELL_UP, GSE15659_RESTING_TREG_VS_NONSUPPRESSIVE_TCELL_UP, GSE17974_IL4_AND_ANTI_IL12_VS_UNTREATED_48H_ACT_CD4_TCELL_DN, GSE2706_R848_VS_R848_AND_LPS_8H_STIM_DC_DN, chr19q13

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
cellular anatomical structure	1

Protein interactions and networks

STRING

732 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SIGLECL1	NTMT2	Q5VVY1	332
SIGLECL1	KLHL11	Q9NVR0	286
SIGLECL1	AK5	Q9Y6K8	242
SIGLECL1	CACNG3	O60359	229
SIGLECL1	ZNF16	P17020	203
SIGLECL1	KCNF1	Q9H3M0	203
SIGLECL1	SCARA3	Q6AZY7	186
SIGLECL1	GPC5	P78333	185
SIGLECL1	FAT3	Q8TDW7	176
SIGLECL1	ARHGAP26	Q9UNA1	171
SIGLECL1	AK1	P00568	166
SIGLECL1	TTR	P02766	166
SIGLECL1	GSX1	Q9H4S2	166
SIGLECL1	BIN1	O00499	166
SIGLECL1	MRLN	P0DMT0	166
SIGLECL1	PRCP	P42785	166
SIGLECL1	ADAM8	P78325	166

IntAct

14 interactions, top by confidence:

A	B	Type	Score
TTMP	SIGLECL1	psi-mi:“MI:0915”(physical association)	0.670
APOD	SIGLECL1	psi-mi:“MI:0915”(physical association)	0.560
EMP3	SIGLECL1	psi-mi:“MI:0915”(physical association)	0.560
SIGLECL1	KIAA1324L	psi-mi:“MI:0914”(association)	0.350
SIGLECL1	RBFOX3	psi-mi:“MI:0914”(association)	0.350
SIGLECL1	ELAPOR2	psi-mi:“MI:0914”(association)	0.350
SIGLECL1	IPO5	psi-mi:“MI:0914”(association)	0.350
APOD	SIGLECL1	psi-mi:“MI:0915”(physical association)	0.000
TTMP	SIGLECL1	psi-mi:“MI:0915”(physical association)	0.000
EMP3	SIGLECL1	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (202): FAM73B (Affinity Capture-MS), TNPO2 (Affinity Capture-MS), VPS8 (Affinity Capture-MS), FAM73A (Affinity Capture-MS), TBC1D22B (Affinity Capture-MS), DFNA5 (Affinity Capture-MS), BTAF1 (Affinity Capture-MS), IPO9 (Affinity Capture-MS), STAG1 (Affinity Capture-MS), MPZL1 (Affinity Capture-MS), RADIL (Affinity Capture-MS), XPO4 (Affinity Capture-MS), KIF14 (Affinity Capture-MS), CWC22 (Affinity Capture-MS), SDK2 (Affinity Capture-MS)

ESM2 similar proteins: A0JNM1, A1L1A6, A6QNY1, A6QQC6, B0CLX4, B2RTN2, B8JI67, D3YX43, O02733, O88324, P01881, P01883, P12342, P21995, P26898, P86176, Q01151, Q0VCB1, Q0VFL4, Q2YDG7, Q3U0X8, Q5RCS3, Q5UKY4, Q6AXW8, Q6PCB8, Q7TMJ8, Q7TQM3, Q7TSN7, Q8BJN4, Q8IW00, Q8N7X8, Q8R526, Q8TBE3, Q8TDX9, Q8VCP9, Q8VD31, Q91V87, Q91ZV2, Q91ZV3, Q96FE7

Diamond homologs: A6NMB1, O15389, O43699, P20138, Q08ET2, Q460M5, Q63994, Q64JA4, Q6ZMC9, Q80TG9, Q80ZE3, Q8N7X8, Q91Y57, Q920G3, Q95LH0, Q96LC7, Q96PQ1, Q96RL6, Q9BE71, Q9NYZ4, Q9ULH4, Q9Y286, Q9Y336, D4ABX8, F1NY98, Q3URE9, Q6AZB0, Q7L985, Q80XU8, Q8K099, Q8VHZ8, Q9ERC8, Q9JMH2, Q9P2V4, P06731, Q9UQ72, D3YXG0, P35329, Q8NDA2, Q96LA5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

27 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	22
Likely benign	4
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

537 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
19:51265462:G:C	W39C	0.980
19:51265462:G:T	W39C	0.980
19:51265430:T:C	F29L	0.973
19:51265432:C:A	F29L	0.973
19:51265432:C:G	F29L	0.973
19:51265460:T:A	W39R	0.965
19:51265460:T:C	W39R	0.965
19:51265547:A:C	S68R	0.964
19:51265549:C:A	S68R	0.964
19:51265549:C:G	S68R	0.964
19:51265431:T:G	F29C	0.948
19:51265436:G:T	G31W	0.937
19:51265418:T:A	C25S	0.935
19:51265419:G:C	C25S	0.935
19:51265418:T:C	C25R	0.928
19:51265437:G:A	G31E	0.921
19:51265554:T:A	I70N	0.916
19:51265424:T:C	C27R	0.915
19:51265540:G:C	W65C	0.911
19:51265540:G:T	W65C	0.911
19:51265437:G:T	G31V	0.909
19:51265431:T:C	F29S	0.904
19:51265394:T:C	C17R	0.902
19:51265461:G:C	W39S	0.902
19:51265394:T:A	C17S	0.901
19:51265395:G:C	C17S	0.901
19:51265554:T:G	I70S	0.900
19:51265426:T:G	C27W	0.895
19:51265554:T:C	I70T	0.894
19:51265541:G:C	A66P	0.892

dbSNP variants (sampled 300 via entrez): RS1000156516 (19:51261764 T>C), RS1000278422 (19:51267716 T>G), RS1000588998 (19:51251341 A>C), RS1000792906 (19:51256325 G>A), RS1000813251 (19:51257295 A>G), RS1001170279 (19:51249910 A>G,T), RS1001261878 (19:51250282 G>A), RS1001526912 (19:51263109 C>G,T), RS1001542339 (19:51252305 AAAAAGAAAAG>A,AAAAAG,AAAAAGAAAAGAAAAG), RS1001565545 (19:51268683 C>A,G), RS1001841106 (19:51255568 A>G), RS1001945125 (19:51264592 A>G), RS1002171263 (19:51251136 G>A,T), RS1002205721 (19:51268366 C>T), RS1002266056 (19:51251324 G>A)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

1 associations (top):

Study	Trait	p-value
GCST001838_9	Palmitic acid (16:0) levels	9.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

6 total (human), top 6 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases mutagenesis	2
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Valproic Acid	decreases methylation	1
Asbestos, Serpentine	decreases methylation	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.