MEIG1

Summary

MEIG1 (meiosis/spermiogenesis associated 1, HGNC:23429) is a protein-coding gene on chromosome 10p13, encoding Meiosis expressed gene 1 protein homolog (Q5JSS6). Essential for spermiogenesis.

Predicted to be involved in cell differentiation. Predicted to act upstream of or within manchette assembly and protein localization. Predicted to be located in cytosol and manchette. Predicted to be active in nucleus.

Source: NCBI Gene 644890 — RefSeq curated summary.

At a glance

• GWAS associations: 2
• Clinical variants (ClinVar): 22 total — 1 pathogenic
• MANE Select transcript: NM_001080836

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23429
Approved symbol	MEIG1
Name	meiosis/spermiogenesis associated 1
Location	10p13
Locus type	gene with protein product
Status	Approved
Aliases	bA2K17.3, SPATA39
Ensembl gene	ENSG00000197889
Ensembl biotype	protein_coding
OMIM	614174
Entrez	644890

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 3 protein_coding_CDS_not_defined

ENST00000378240, ENST00000407572, ENST00000467536, ENST00000477770, ENST00000496225, ENST00000891559, ENST00000934258, ENST00000948371

RefSeq mRNA: 1 — MANE Select: NM_001080836 NM_001080836

CCDS: CCDS31151

Canonical transcript exons

ENST00000407572 — 3 exons

Exon	Start	End
ENSE00001563614	14966440	14966606
ENSE00003849941	14959388	14959557
ENSE00003851029	14972513	14972857

Expression profiles

Bgee: expression breadth ubiquitous, 165 present calls, max score 89.35.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7988 / max 26.6140, expressed in 451 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103990	0.6852	405
103989	0.0953	32
103991	0.0182	5

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.35	gold quality
bronchial epithelial cell	CL:0002328	87.31	gold quality
bronchus	UBERON:0002185	85.23	gold quality
right uterine tube	UBERON:0001302	83.70	gold quality
left testis	UBERON:0004533	83.49	gold quality
sperm	CL:0000019	83.18	gold quality
right testis	UBERON:0004534	82.97	gold quality
testis	UBERON:0000473	80.78	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.10	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.04	gold quality
pancreatic ductal cell	CL:0002079	72.36	silver quality
calcaneal tendon	UBERON:0003701	69.31	gold quality
cortical plate	UBERON:0005343	69.03	gold quality
mucosa of paranasal sinus	UBERON:0005030	68.61	silver quality
nucleus accumbens	UBERON:0001882	67.95	gold quality
ileal mucosa	UBERON:0000331	67.46	silver quality
adrenal tissue	UBERON:0018303	67.00	gold quality
caudate nucleus	UBERON:0001873	65.83	gold quality
hypothalamus	UBERON:0001898	65.81	gold quality
fallopian tube	UBERON:0003889	65.57	gold quality
adenohypophysis	UBERON:0002196	65.47	gold quality
putamen	UBERON:0001874	65.37	gold quality
anterior cingulate cortex	UBERON:0009835	64.64	gold quality
islet of Langerhans	UBERON:0000006	64.55	gold quality
mucosa of transverse colon	UBERON:0004991	64.45	gold quality
right adrenal gland cortex	UBERON:0035827	64.17	gold quality
Brodmann (1909) area 9	UBERON:0013540	64.04	gold quality
pituitary gland	UBERON:0000007	63.97	gold quality
amygdala	UBERON:0001876	63.96	gold quality
right adrenal gland	UBERON:0001233	63.64	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

18 targeting MEIG1, 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-1252-5P	100.00	69.80	2774
HSA-MIR-1184	99.99	68.19	1458
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-5010-3P	99.83	70.60	2357
HSA-MIR-5093	99.67	69.26	2291
HSA-MIR-3158-5P	99.65	67.51	1763
HSA-MIR-548AV-5P	99.60	70.84	2107
HSA-MIR-548K	99.60	70.84	2107
HSA-MIR-4761-5P	99.51	66.69	804
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-548AV-3P	99.43	68.50	1721
HSA-MIR-183-3P	99.41	69.41	1598
HSA-MIR-1272	99.34	68.79	878
HSA-MIR-3154	98.94	66.55	1455
HSA-MIR-5000-3P	98.79	65.63	1251
HSA-MIR-4436A	98.05	64.83	1140
HSA-MIR-4700-3P	97.74	68.64	1014
HSA-MIR-4771	97.43	67.69	596

Literature-anchored findings (GeneRIF, showing 2)

• Crystal structure of human PACRG in complex with MEIG1 reveals roles in axoneme formation and tubulin binding. (PMID:33529594)
• Polymorphisms in the HSF2, LRRC6, MEIG1 and PTIP genes correlate with sperm motility in idiopathic infertility. (PMID:35768906)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	meig1	ENSDARG00000045705
mus_musculus	Meig1	ENSMUSG00000026650
rattus_norvegicus	Meig1	ENSRNOG00000016283

Protein

Protein identifiers

Meiosis expressed gene 1 protein homolog — Q5JSS6 (reviewed: Q5JSS6)

All UniProt accessions (1): Q5JSS6

UniProt curated annotations — full annotation on UniProt →

Function. Essential for spermiogenesis.

Subunit / interactions. Interacts with PACRG. Interacts with MORN3.

Similarity. Belongs to the MEIG1 family.

RefSeq proteins (1): NP_001074305* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR020186	Meiosis-expressed_gene_1	Family

Pfam: PF15163

UniProt features (10 total): strand 4, helix 3, chain 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
6NEP	X-RAY DIFFRACTION	2.1
6NDU	X-RAY DIFFRACTION	2.1
6UCC	X-RAY DIFFRACTION	2.6

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5JSS6-F1	85.79	0.25

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 68 (showing top): GOBP_MALE_GAMETE_GENERATION, chr10p13, GOBP_CILIUM_ORGANIZATION, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GOBP_ORGANELLE_ASSEMBLY, GOBP_CELLULAR_PROCESS_INVOLVED_IN_REPRODUCTION_IN_MULTICELLULAR_ORGANISM, GOBP_MICROTUBULE_BUNDLE_FORMATION, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOBP_MOTILE_CILIUM_ASSEMBLY, GOBP_CELL_PROJECTION_ORGANIZATION, GOBP_AXONEME_ASSEMBLY, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED

GO Biological Process (5): sperm axoneme assembly (GO:0007288), intracellular protein localization (GO:0008104), manchette assembly (GO:1905198), spermatogenesis (GO:0007283), cell differentiation (GO:0030154)

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

GO Cellular Component (3): manchette (GO:0002177), nucleus (GO:0005634), cytosol (GO:0005829)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
developmental process involved in reproduction	2
cellular anatomical structure	2
axoneme assembly	1
sperm flagellum assembly	1
macromolecule localization	1
spermatid development	1
cellular component assembly	1
male gamete generation	1
cellular developmental process	1
binding	1
microtubule cytoskeleton	1
intracellular membrane-bounded organelle	1
cytoplasm	1

Protein interactions and networks

STRING

548 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MEIG1	SPAG6	O75602	966
MEIG1	SPAG16	Q8N0X2	961
MEIG1	PACRG	Q96M98	596
MEIG1	FER1L6	Q2WGJ9	580
MEIG1	PACRGL	Q8N7B6	564
MEIG1	TEKT2	Q9UIF3	471
MEIG1	TEX38	Q6PEX7	465
MEIG1	DYNC2LI1	Q8TCX1	462
MEIG1	DYNLRB2	Q8TF09	454
MEIG1	CCDC166	P0CW27	447
MEIG1	IMMP2L	Q96T52	419
MEIG1	TOP3A	Q13472	410
MEIG1	SCN7A	Q01118	405
MEIG1	FREY1	C9JXX5	403
MEIG1	FAM194C	Q8ND61	397

IntAct

11 interactions, top by confidence:

A	B	Type	Score
	MEIG1	psi-mi:“MI:0915”(physical association)	0.560
MEIG1	PACRG	psi-mi:“MI:0915”(physical association)	0.560
PACRG	MEIG1	psi-mi:“MI:0915”(physical association)	0.000
MEIG1		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (3): MEIG1 (Two-hybrid), MEIG1 (Two-hybrid), MEIG1 (Affinity Capture-MS)

ESM2 similar proteins: A5VR02, A6U863, A7SMR0, A7WQL9, B2S675, B7HHG6, C0RJJ7, C3MAY4, C4Y451, D2Y494, O10313, O20162, O28329, P00465, P03502, P03715, P05074, P12593, P12597, P12599, P12731, P13327, P24646, P27970, P27979, P66488, P66489, P66490, Q01025, Q02840, Q03EC0, Q0ANQ4, Q11HQ6, Q2YM07, Q32LI5, Q3ISB2, Q54J26, Q57CR2, Q5I134, Q5JSS6

Diamond homologs: A7SMR0, A7WQL9, Q32LI5, Q5JSS6, Q5RGE4, Q61845, Q6PB04

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	18
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
1047870	GRCh37/hg19 10p14-13(chr10:9137489-17227168)	Pathogenic

SpliceAI

742 predictions. Top by Δscore:

Variant	Effect	Δscore
10:14959630:G:GT	donor_gain	1.0000
10:14959690:G:GT	donor_gain	1.0000
10:14962133:T:TA	acceptor_gain	1.0000
10:14959531:GA:G	donor_gain	0.9900
10:14959540:G:GG	donor_gain	0.9900
10:14959555:GGG:G	donor_gain	0.9900
10:14959556:GGG:G	donor_gain	0.9900
10:14959731:G:T	donor_gain	0.9900
10:14962138:C:G	acceptor_gain	0.9900
10:14972503:T:A	acceptor_gain	0.9900
10:14972507:GTGCA:G	acceptor_loss	0.9900
10:14972508:TGCA:T	acceptor_loss	0.9900
10:14972509:GCAG:G	acceptor_loss	0.9900
10:14972510:CAG:C	acceptor_loss	0.9900
10:14972512:G:A	acceptor_loss	0.9900
10:14972512:GGTA:G	acceptor_gain	0.9900
10:14959630:G:T	donor_gain	0.9800
10:14959691:G:T	donor_gain	0.9800
10:14962137:A:AG	acceptor_gain	0.9800
10:14972496:T:TA	acceptor_gain	0.9800
10:14959782:G:GT	donor_gain	0.9700
10:14959917:G:GG	donor_gain	0.9700
10:14962134:G:A	acceptor_gain	0.9700
10:14970437:T:TA	donor_gain	0.9700
10:14959467:C:T	donor_gain	0.9600
10:14959939:G:GT	donor_gain	0.9600
10:14970344:TCTAG:T	donor_gain	0.9600
10:14970424:G:GT	donor_gain	0.9600
10:14972511:A:AG	acceptor_gain	0.9600
10:14972512:G:GG	acceptor_gain	0.9600

AlphaMissense

579 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:14966546:A:C	R26S	0.992
10:14966546:A:T	R26S	0.992
10:14966545:G:C	R26T	0.991
10:14972522:T:A	W50R	0.989
10:14972522:T:C	W50R	0.989
10:14966548:T:C	F27S	0.987
10:14972541:T:A	V56E	0.985
10:14972550:T:A	L59H	0.983
10:14966556:G:C	A30P	0.982
10:14966562:T:G	Y32D	0.982
10:14966563:A:C	Y32S	0.982
10:14972550:T:C	L59P	0.982
10:14966580:T:G	Y38D	0.980
10:14966581:A:C	Y38S	0.980
10:14972545:G:C	K57N	0.980
10:14972545:G:T	K57N	0.980
10:14972570:T:C	F66L	0.980
10:14972572:C:A	F66L	0.980
10:14972572:C:G	F66L	0.980
10:14966517:T:A	W17R	0.979
10:14966517:T:C	W17R	0.979
10:14966557:C:A	A30E	0.979
10:14966580:T:C	Y38H	0.974
10:14972593:G:C	R73S	0.974
10:14972593:G:T	R73S	0.974
10:14966544:A:G	R26G	0.971
10:14966566:G:C	R33P	0.971
10:14966547:T:C	F27L	0.970
10:14966549:T:A	F27L	0.970
10:14966549:T:G	F27L	0.970

dbSNP variants (sampled 300 via entrez): RS1000006787 (10:14984513 T>C), RS1000008995 (10:14973097 C>A), RS1000147156 (10:14953027 G>A,C,T), RS1000187447 (10:14962542 T>C), RS1000299782 (10:14967969 C>A), RS1000579147 (10:14960877 A>T), RS1000617560 (10:14963175 C>A), RS1000642770 (10:14962277 G>C), RS1000824403 (10:14958351 C>A), RS1000867288 (10:14976891 G>C), RS1000923023 (10:14961264 A>G), RS1001014511 (10:14974231 T>G), RS1001112117 (10:14979566 A>G,T), RS1001173206 (10:14958100 T>C), RS1001286947 (10:14971192 A>G)

Disease associations

OMIM: gene MIM:614174 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

Study	Trait	p-value
GCST008359_6	Response to cognitive-behavioural therapy in anxiety disorder	4.000000e-06
GCST009391_63	Metabolite levels	6.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0007820	cognitive behavioural therapy
EFO:0010352	diacylglycerol 34:1 measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
pirinixic acid	affects binding, decreases expression, increases activity	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
Benzo(a)pyrene	increases methylation	1
Formaldehyde	increases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Silicon Dioxide	decreases expression	1
Tobacco Smoke Pollution	affects expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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