Slamf6 MGI Mouse Gene Detail - MGI:1353620 - SLAM family member 6

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Slamf6 Gene Detail

Symbol

Slamf6
Name

SLAM family member 6
Synonyms

KAL1, KAL1b, Ly108, NTB-A, SF2000

Feature Type

protein coding gene
IDs

MGI:1353620
NCBI Gene: 30925
Alliance

gene page
Transcription Start Sites

9 TSS
Candidate for QTL

2 QTL

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Sequence Map

Chr1:171745002-171776525 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 79.54 cM
Mapping Data

7 experiments

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SNPs within 2kb

851 from dbSNP Build 142
Strain Annotations

18
PCR

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_1353620	protein coding gene	Chr1:171745002-171780737 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0016773	protein coding gene	Chr1:177747465-177791073 (+)
A/J	MGP_AJ_G0016752	protein coding gene	Chr1:170483545-170519528 (+)
AKR/J	MGP_AKRJ_G0016718	protein coding gene	Chr1:175631917-175668504 (+)
BALB/cJ	MGP_BALBcJ_G0016713	protein coding gene	Chr1:171030146-171066874 (+)
C3H/HeJ	MGP_C3HHeJ_G0016537	protein coding gene	Chr1:176207251-176246509 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0017175	protein coding gene	Chr1:183652514-183689653 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014881	protein coding gene	Chr1:162187514-162220408 (+)
CAST/EiJ	MGP_CASTEiJ_G0016117	protein coding gene	Chr1:175553822-175588925 (+)
CBA/J	MGP_CBAJ_G0016511	protein coding gene	Chr1:190192999-190226689 (+)
DBA/2J	MGP_DBA2J_G0016618	protein coding gene	Chr1:169424226-169459148 (+)
FVB/NJ	MGP_FVBNJ_G0016615	protein coding gene	Chr1:167678291-167713361 (+)
LP/J	MGP_LPJ_G0016689	protein coding gene	Chr1:178838188-178873465 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0016642	protein coding gene	Chr1:197461221-197497812 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0017211	protein coding gene	Chr1:175489355-175530911 (+)
PWK/PhJ	MGP_PWKPhJ_G0015903	protein coding gene	Chr1:168791017-168826564 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0015685	protein coding gene	Chr1:174428120-174461634 (+)
WSB/EiJ	MGP_WSBEiJ_G0016179	protein coding gene	Chr1:175657809-175691329 (+)

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Human Ortholog

SLAMF6, SLAM family member 6

Vertebrate Orthologs

3

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SLAMF6, SLAM family member 6
Synonyms

CD352, KALI, KALIb, Ly108, NTB-A, NTBA, SF2000
Links

HGNC:21392

NCBI Gene ID: 114836

neXtProt AC: NX_Q96DU3

UniProt: Q96DU3
Chr Location

1q23.2-q23.3; chr1:160485030-160523262 (-) GRCh38

MGI Vertebrate Homology

Slamf6 stringent orthology
1 human;1 mouse;1 rat;1 zebrafish
HCOP

vertebrate homology predictions: SLAMF6
Gene Tree

Slamf6

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Phenotype Summary

12 phenotypes from 2 alleles in 3 genetic backgrounds
1 phenotype from multigenic genotypes
27 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

13
Chemically induced (other)

2
Endonuclease-mediated

2
Targeted

9
Genomic Mutations

3 involving Slamf6
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

33 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for one null allele show no overt phenotype. Mice homozygous for another null allele show impaired IL-4 production by CD4+ T cells, reduced inflammatory response to L. mexicana infection, high susceptibility to S. typhimurium infection, and defective neutrophil bactericidal activity.

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All GO Annotations

13
GO References

5

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

706
cDNA Data

23

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

67
RefSeq

13
UniProt

6
CCDS

CCDS15504.1, CCDS83638.1, CCDS83639.1

Ensembl

ENSMUSG00000015314 (Evidence)
NCBI Gene

30925

Representative Sequences				Length	Strain/Species	Flank
	genomic	30925	NCBI Gene Model \| MGI Sequence Detail	31524	C57BL/6J	± kb
	transcript	NM_030710	RefSeq \| MGI Sequence Detail	2560	ZRU/MplStud
	polypeptide	Q9ET39	UniProt \| EBI \| MGI Sequence Detail	351	Not Applicable

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UniProt

6 Sequences
Protein Ontology

PR:000014913 SLAM family member 6

(term hierarchy)
InterPro Domains

IPR007110 Immunoglobulin-like domain

IPR036179 Immunoglobulin-like domain superfamily

IPR013783 Immunoglobulin-like fold

IPR013106 Immunoglobulin V-set domain
GlyGen

Q9ET39 9 sites

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All nucleic 24

cDNA 23

Primer pair 1

Microarray probesets 6

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Summaries

All 63

Gene Ontology 5

Phenotypes 27
Earliest

J:60849 Peck SR, et al., Ly108: a new member of the mouse CD2 family of cell surface proteins. Immunogenetics. 2000 Nov;52(1-2):63-72
Latest

J:327496 Hasim MS, et al., When killers become thieves: Trogocytosed PD-1 inhibits NK cells in cancer. Sci Adv. 2022 Apr 15;8(15):eabj3286

TSS for Slamf6:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr10148	Chr1:171745005-171745039 (+)	20 bp
Tssr10149	Chr1:171745056-171745070 (+)	61 bp
Tssr10150	Chr1:171745079-171745084 (+)	80 bp
Tssr10151	Chr1:171745235-171745275 (+)	253 bp
Tssr10152	Chr1:171745291-171745298 (+)	293 bp
Tssr10153	Chr1:171745443-171745450 (+)	445 bp
Tssr10154	Chr1:171747000-171747008 (+)	2,002 bp
Tssr10155	Chr1:171747047-171747062 (+)	2,053 bp
Tssr10156	Chr1:171755560-171755563 (+)	10,560 bp

Slamf6 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Nktcn1	Chr1, 76.25 cM	Chr1:168186243-171632257	J:137521	Microarray analysis was performed on thymus RNA from 4 week old NOD.Nkrp1.Nkt1 congenic animals and NOD.Nkrp1 congenic animals to screen candidate genes for Nktcn1. The NOD.Nkrp1 congenic carries C57BL/6J-derived DNA from D6Mit105 (45.5 cM) toD6Mit135 (62.3 cM) on a NOD genetic background. The NOD.Nkrp.Nkt1 congenic carries C57BL/6J-derived DNA from D1Mit369 (73 cM) to D1Mit155 (telomere) on a NOD genetic background in addition to the NOD-derived chromosome 6 interval. The formal QTL designation for Nkt1 is Nktcn1. Nkrp1 is synonymous with Klrb1c. Previously identified lupus susceptibility locus Sle1b (89.5 cM) maps near Nktcn1. Twenty-one genes displaying expression differences between NOD and C57BL/6J mapped to the Nktcn1 region, 15of which are located in the 95% confidence interval. The most promising candidate genes for controlling NKT cell number are Slamf1 (93.3 cM) and Slamf6 (89.5 cM). Gene expression of Slamf1 and Slamf6 was examined in thymic and splenic lymphocytes from congenic animals. It was observed that NOD.Nkrp.Nkt1 animals expressed significantly higher amounts of SLAM proteins on cell sufaces compared to NOD.Nkt1 parentals. Authors hypothesize control of NKT cell numbers may be mediated by differentialexpression of Slamf1 with additionial influence by Slamf6.
Sle1b	Chr1, 75.10 cM		J:94686	Congenic and physical mapping was used to show that Sle1b mapped within an interval containing SLAM family members ordered as Cd244 - Ly9 - Slamf7 - Cd48 - Slamf1 - Cd84 - Slamf6. Haplotype analysis of the aformentioned region were suggestive that the markers contained within the region as contributing to the Sle1b phenotype. The strongest contribution may come from Slamf6.

*cM position of peak correlated region/marker

Contributing Projects: Mouse Genome Database (MGD), Gene Expression Database (GXD), Mouse Models of Human Cancer database (MMHCdb) (formerly Mouse Tumor Biology (MTB)), Gene Ontology (GO)
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