Spata46 MGI Mouse Gene Detail - MGI:1924175 - spermatogenesis associated 46

Symbol

Spata46
Name

spermatogenesis associated 46
Synonyms

1700015E13Rik

Feature Type

protein coding gene
IDs

MGI:1924175
NCBI Gene: 76925
Alliance

genome feature page
Transcription Start Sites

4 TSS

Sequence Map

Chr1:170136388-170139694 bp, + strand
From NCBI annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 76.84 cM
Mapping Data

1 experiment

SNPs within 2kb

218 from dbSNP Build 142
Strain Annotations

19

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1924175	protein coding gene	Chr1:170136372-170139694 (+)
129S1/SvImJ	ENSMUSG00200043265	protein coding gene	Chr1:167600266-167603572 (+)
A/J	ENSMUSG00195045819	protein coding gene	Chr1:166919563-166922872 (+)
AKR/J	ENSMUSG00220025665	protein coding gene	Chr1:166628039-166631361 (+)
BALB/cJ	ENSMUSG00180043552	protein coding gene	Chr1:167195846-167199168 (+)
C3H/HeJ	ENSMUSG00175047017	protein coding gene	Chr1:167255853-167259159 (+)
C57BL/6NJ	ENSMUSG00215044518	protein coding gene	Chr1:167077140-167080462 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014842	protein coding gene	Chr1:160564254-160567536 (+)
CAST/EiJ	ENSTCUG00005045337	protein coding gene	Chr1:165586136-165589447 (+)
CBA/J	ENSMUSG00210038203	protein coding gene	Chr1:167160922-167164244 (+)
DBA/2J	ENSMUSG00185011713	protein coding gene	Chr1:171377718-171381040 (+)
FVB/NJ	ENSMUSG00205025695	protein coding gene	Chr1:166118003-166121309 (+)
JF1/MsJ	ENSUMUG00000004649	protein coding gene	Chr1:170521037-170524359 (+)
LP/J	ENSMUSG00230023467	protein coding gene	Chr1:170987070-170990699 (+)
NOD/ShiLtJ	ENSMUSG00190028356	protein coding gene	Chr1:166918603-166921912 (+)
NZO/HlLtJ	ENSMUSG00225003408	protein coding gene	Chr1:174593348-174596980 (+)
PWK/PhJ	ENSLUMG00010027412	protein coding gene	Chr1:165911950-165915270 (+)
SPRET/EiJ	ENSMSPG00010045018	protein coding gene	Chr1:169465530-169468849 (+)
WSB/EiJ	ENSIUOG00005035224	protein coding gene	Chr1:166327292-166330602 (+)

Human Ortholog

SPATA46, spermatogenesis associated 46

Vertebrate Orthologs

2

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SPATA46, spermatogenesis associated 46
Synonyms

C1orf111, HSD20, TEKT2BP2
Links

HGNC:27648

NCBI Gene ID: 284680

UniProt: Q5T0L3
Chr Location

1q23.3; chr1:162373203-162376874 (-) GRCh38

MGI Vertebrate Homology

Spata46 stringent orthology
1 human;1 mouse;1 rat
HCOP

vertebrate homology predictions: SPATA46
Gene Tree

Spata46

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Phenotype Summary

18 phenotypes from 2 alleles in 2 genetic backgrounds
7 phenotype references

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

4
Chemically induced (other)

2
Endonuclease-mediated

1
Targeted

1
Genomic Mutations

2 involving Spata46
Incidental Mutations

Mutagenetix , APF
Find Mice (IMSR)

9 strains or lines available
Comparison Matrix

Gene Expression + Phenotype

Mice homozygous for a knock-out allele exhibit reduced male fertility, teratozoospermia characterized by sperm head malformations, and impaired fertilization with lower rates of sperm-egg fusion.

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All GO Annotations

7
GO References

4

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

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

597
cDNA Data

18

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

Other Mouse Links

Allen Institute

GEO

Expression Atlas

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All Sequences

33
RefSeq

2
UniProt

1
CCDS

CCDS15471.1

Ensembl

ENSMUSG00000042800 (Evidence)
NCBI Gene

76925

			Length	Strain/Species	Flank
genomic	76925	NCBI Gene Model \| MGI Sequence Detail	3307	C57BL/6J	± kb
transcript	NM_001039593	RefSeq \| MGI Sequence Detail	755	C57BL/6
polypeptide	Q4FZF2	UniProt \| EBI \| MGI Sequence Detail	204	Not Applicable

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UniProt

1 Sequence
Protein Ontology

PR:000059820 spermatogenesis-associated protein 46

(term hierarchy)
InterPro Domains

IPR040879 Spermatogenesis-associated protein 46-like

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All nucleic 18

cDNA 18

Microarray probesets 5

Summaries

All 30

Gene Ontology 4

Phenotypes 7
Earliest

J:65060 Kawai J, et al., Functional annotation of a full-length mouse cDNA collection. Nature. 2001 Feb 8;409(6821):685-90
Latest

J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Spata46:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr9922	Chr1:170136371-170136397 (+)	-4 bp
Tssr9923	Chr1:170136405-170136453 (+)	41 bp
Tssr9924	Chr1:170136459-170136462 (+)	73 bp
Tssr9925	Chr1:170136902-170136912 (+)	519 bp

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)
Citing These Resources Funding Information Warranty Disclaimer, Privacy Notice, Licensing, & Copyright Send questions and comments to User Support.	last database update 09/08/2026 MGI 6.24