IQCM

Summary

IQCM (IQ motif containing M, HGNC:53443) is a protein-coding gene on chromosome 4q31.23, encoding IQ domain-containing protein M (A0A1B0GVH7).

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_001363507

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:53443
Approved symbol	IQCM
Name	IQ motif containing M
Location	4q31.23
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000234828
Ensembl biotype	protein_coding
Entrez	285423

Gene structure

Transcript identifiers

Ensembl transcripts: 6 — 3 protein_coding_CDS_not_defined, 2 protein_coding, 1 nonsense_mediated_decay

ENST00000502345, ENST00000508106, ENST00000510975, ENST00000511993, ENST00000636414, ENST00000636793

RefSeq mRNA: 9 — MANE Select: NM_001363507 NM_001363507, NM_001363509, NM_001378177, NM_001378178, NM_001378179, NM_001378180, NM_001378181, NM_001378182, NM_001378184

CCDS: CCDS87270, CCDS87271

Canonical transcript exons

ENST00000636793 — 14 exons

Exon	Start	End
ENSE00002046780	149815311	149815348
ENSE00002071575	149351709	149352066
ENSE00002074637	149553143	149553287
ENSE00003791741	149548455	149548589
ENSE00003794447	149686378	149686468
ENSE00003795394	149587930	149587997
ENSE00003796078	149433396	149433557
ENSE00003796169	149621129	149621244
ENSE00003796207	149742655	149742739
ENSE00003799238	149682118	149682206
ENSE00003799639	149735376	149735458
ENSE00003800376	149563692	149563890
ENSE00003801201	149733244	149733508
ENSE00003909358	149815600	149815843

Expression profiles

Bgee: expression breadth broad, 25 present calls, max score 80.93.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0144 / max 12.1793, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
54295	0.0064	2
54294	0.0044	3
203374	0.0036	3

Top tissues by expression

215 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	80.93	gold quality
colonic epithelium	UBERON:0000397	70.62	gold quality
left testis	UBERON:0004533	68.08	gold quality
testis	UBERON:0000473	66.83	gold quality
sperm	CL:0000019	66.58	silver quality
right testis	UBERON:0004534	66.54	gold quality
mucosa of transverse colon	UBERON:0004991	61.58	gold quality
rectum	UBERON:0001052	56.68	gold quality
transverse colon	UBERON:0001157	50.17	gold quality
bone marrow cell	CL:0002092	48.09	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	47.63	silver quality
buccal mucosa cell	CL:0002336	46.11	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
lower lobe of lung	UBERON:0008949	42.81	silver quality
secondary oocyte	CL:0000655	42.57	gold quality
skeletal muscle tissue	UBERON:0001134	41.77	gold quality
tonsil	UBERON:0002372	41.57	silver quality
vastus lateralis	UBERON:0001379	41.41	gold quality
subthalamic nucleus	UBERON:0001906	41.41	gold quality
quadriceps femoris	UBERON:0001377	41.37	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality
palpebral conjunctiva	UBERON:0001812	41.10	gold quality
mucosa of paranasal sinus	UBERON:0005030	40.98	gold quality
caecum	UBERON:0001153	40.92	gold quality
large intestine	UBERON:0000059	40.91	gold quality
colon	UBERON:0001155	40.75	gold quality
amniotic fluid	UBERON:0000173	40.69	gold quality
colonic mucosa	UBERON:0000317	40.64	gold quality
jejunal mucosa	UBERON:0000399	40.59	gold quality
biceps brachii	UBERON:0001507	40.57	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.03

Regulation

Is transcription factor: no

Cross-species orthologs

6 orthologs

Organism	Symbol	Gene ID
mus_musculus	Iqcm	ENSMUSG00000031620
rattus_norvegicus		ENSRNOG00000071763
rattus_norvegicus		ENSRNOG00000073983
rattus_norvegicus		ENSRNOG00000074043
rattus_norvegicus		ENSRNOG00000085366
rattus_norvegicus		ENSRNOG00000090730

Protein

Protein identifiers

IQ domain-containing protein M — A0A1B0GVH7 (reviewed: A0A1B0GVH7)

All UniProt accessions (3): A0A1B0GVH7, A0A1B0GUF7, A0A1B0GVS1

RefSeq proteins (9): NP_001350436, NP_001350438, NP_001365106, NP_001365107, NP_001365108, NP_001365109, NP_001365110, NP_001365111, NP_001365113 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000048	IQ_motif_EF-hand-BS	Binding_site

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1B0GVH7-F1	61.77	0.14

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 8 (showing top): GSE45365_HEALTHY_VS_MCMV_INFECTION_CD8_TCELL_IFNAR_KO_UP, GSE12366_GC_VS_MEMORY_BCELL_DN, chr4q31, KANNAN_BLOOD_2012_2013_TIV_AGE_65PLS_REVACCINATED_IN_6_9_MO_VS_REVACCINATED_IN_12_13_MO_UP, GSE26928_EFF_MEM_VS_CENTR_MEM_CD4_TCELL_DN, GSE2706_UNSTIM_VS_2H_R848_DC_DN, GSE26488_HDAC7_KO_VS_VP16_TRANSGENIC_HDAC7_KO_DOUBLE_POSITIVE_THYMOCYTE_UP, GSE30971_2H_VS_4H_LPS_STIM_MACROPHAGE_WBP7_HET_DN

GO Biological Process (0):

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

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

90 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
IQCM	CDH11	P55287	419
IQCM	ANAPC13	Q9BS18	402
IQCM	UQCC1	Q9NVA1	370
IQCM	CABLES1	Q8TDN4	368
IQCM	COL6A5	A8TX70	358
IQCM	LCORL	Q8N3X6	354
IQCM	ATF7	P17544	329
IQCM	DNM3	Q9UQ16	295
IQCM	DDX3Y	O15523	286
IQCM	MED6	O75586	278
IQCM	MT3	P25713	266
IQCM	NAA11	Q9BSU3	257
IQCM	UGT2B17	O75795	250
IQCM	ADGRG6	Q86SQ4	247
IQCM	CDK7	P50613	189

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GUX0, A0A1B0GVH7, A0A3Q1LFK7, A0A3Q1MT14, A2BFC9, A4QMS7, A6NJV1, A6NL82, A8QW39, B0UXH9, B5X5D0, B9EJX3, E1B9R1, F1MMV1, F1P3Y5, Q1JPL0, Q2KI52, Q32KQ1, Q32L72, Q32P67, Q3SZR5, Q4R2Y2, Q5BN45, Q5BN46, Q5NC57, Q5RHU7, Q5SUV2, Q5SVJ3, Q5VZQ5, Q69CM7, Q6AYM0, Q6NXP0, Q6P3G4, Q6ZVS7, Q8CDT5, Q8CDU5, Q8N7U6, Q8N865, Q8ND61

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

3327 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:149553161:A:G	W359R	0.996
4:149553161:A:T	W359R	0.996
4:149433441:A:G	W449R	0.993
4:149433441:A:T	W449R	0.993
4:149553151:C:G	R362P	0.993
4:149563806:G:C	F278L	0.993
4:149563806:G:T	F278L	0.993
4:149563808:A:G	F278L	0.993
4:149433499:A:C	F429L	0.992
4:149433499:A:T	F429L	0.992
4:149433501:A:G	F429L	0.992
4:149433500:A:G	F429S	0.989
4:149553147:T:A	K363N	0.988
4:149553147:T:G	K363N	0.988
4:149563720:C:G	R307P	0.988
4:149563815:G:C	F275L	0.988
4:149563815:G:T	F275L	0.988
4:149563817:A:G	F275L	0.988
4:149548573:A:C	F370L	0.987
4:149548573:A:T	F370L	0.987
4:149548575:A:G	F370L	0.987
4:149433439:C:A	W449C	0.985
4:149433439:C:G	W449C	0.985
4:149563807:A:G	F278S	0.983
4:149553159:C:A	W359C	0.982
4:149553159:C:G	W359C	0.982
4:149563692:C:A	K316N	0.981
4:149563692:C:G	K316N	0.981
4:149563819:A:C	I274S	0.981
4:149563819:A:G	I274T	0.980

dbSNP variants (sampled 300 via entrez): RS1000006960 (4:149668333 C>T), RS1000008463 (4:149709225 C>A), RS1000025917 (4:149645961 C>A), RS1000026078 (4:149517222 C>T), RS1000028937 (4:149534519 A>C), RS1000038372 (4:149661301 T>G), RS1000042433 (4:149376416 A>G), RS1000043510 (4:149751624 G>T), RS1000050962 (4:149618325 A>G,T), RS1000058213 (4:149583813 T>C), RS1000058945 (4:149362065 G>C), RS1000061165 (4:149453286 T>C), RS1000076621 (4:149711026 A>C), RS1000079009 (4:149366162 G>A), RS1000092164 (4:149796206 C>A,G)

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

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression, increases expression	2

Clinical trials (associated diseases)

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