KANTR

Summary

KANTR (KANTR integral membrane protein, HGNC:49510) is a protein-coding gene on chromosome Xp11.22, encoding KANTR integral membrane protein (A0A1W2PQU2).

This gene is thought to produce a functional long non-coding RNA. Mutation of this locus in mouse causes tremors and spastic movements, suggesting a role for this gene in neurological development or function.

Source: NCBI Gene 102723508 — RefSeq curated summary.

At a glance

• MANE Select transcript: NM_001397448

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:49510
Approved symbol	KANTR
Name	KANTR integral membrane protein
Location	Xp11.22
Locus type	gene with protein product
Status	Approved
Aliases	Spasm
Ensembl gene	ENSG00000232593
Ensembl biotype	protein_coding
OMIM	301019
Entrez	102723508

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 4 protein_coding_CDS_not_defined, 3 protein_coding

ENST00000366185, ENST00000603385, ENST00000604062, ENST00000604849, ENST00000605526, ENST00000860106, ENST00000860107

RefSeq mRNA: 5 — MANE Select: NM_001397448 NM_001397448, NM_001397450, NM_001397451, NM_001397452, NM_001397453

CCDS: CCDS94609

Canonical transcript exons

ENST00000604062 — 3 exons

Exon	Start	End
ENSE00003574952	53094142	53094284
ENSE00003650261	53123469	53127438
ENSE00003670283	53099472	53099608

Expression profiles

Bgee: expression breadth ubiquitous, 243 present calls, max score 91.30.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.6398 / max 174.7963, expressed in 1586 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
196418	6.8465	1442
196419	1.5964	923
196417	0.1970	85

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
upper arm skin	UBERON:0004263	91.30	silver quality
cerebellar hemisphere	UBERON:0002245	90.30	gold quality
cerebellar cortex	UBERON:0002129	90.19	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.78	gold quality
cerebellum	UBERON:0002037	89.68	gold quality
epithelial cell of pancreas	CL:0000083	88.35	silver quality
adenohypophysis	UBERON:0002196	85.93	gold quality
pituitary gland	UBERON:0000007	85.92	gold quality
cortical plate	UBERON:0005343	84.96	gold quality
cerebellar vermis	UBERON:0004720	84.03	gold quality
left ovary	UBERON:0002119	83.50	gold quality
hypothalamus	UBERON:0001898	83.12	gold quality
right ovary	UBERON:0002118	82.91	gold quality
primary visual cortex	UBERON:0002436	82.83	gold quality
Brodmann (1909) area 9	UBERON:0013540	82.81	gold quality
calcaneal tendon	UBERON:0003701	82.73	gold quality
skin of abdomen	UBERON:0001416	82.68	gold quality
nucleus accumbens	UBERON:0001882	82.64	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	82.55	gold quality
caudate nucleus	UBERON:0001873	82.30	gold quality
right uterine tube	UBERON:0001302	82.19	gold quality
amygdala	UBERON:0001876	81.89	gold quality
uterine cervix	UBERON:0000002	81.84	gold quality
skin of leg	UBERON:0001511	81.81	gold quality
anterior cingulate cortex	UBERON:0009835	81.77	gold quality
tibial nerve	UBERON:0001323	81.74	gold quality
body of uterus	UBERON:0009853	81.71	gold quality
tendon	UBERON:0000043	81.65	gold quality
quadriceps femoris	UBERON:0001377	81.56	silver quality
endocervix	UBERON:0000458	81.51	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	5.28

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Kantr	ENSMUSG00000087403
rattus_norvegicus	Kantr	ENSRNOG00000083228

Protein

Protein identifiers

KANTR integral membrane protein — A0A1W2PQU2 (reviewed: A0A1W2PQU2)

All UniProt accessions (1): A0A1W2PQU2

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

RefSeq proteins (5): NP_001384377, NP_001384379, NP_001384380, NP_001384381, NP_001384382 (=MANE)

Domains & families (InterPro)

UniProt features (5 total): topological domain 2, signal peptide 1, chain 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A0A1W2PQU2-F1	80.66	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 12 (showing top): STARK_PREFRONTAL_CORTEX_22Q11_DELETION_DN, CUI_TCF21_TARGETS_2_UP, chrXp11, PRKDC_TARGET_GENES, ZNF30_TARGET_GENES, ZNF350_TARGET_GENES, ZNF768_TARGET_GENES, ZNF92_TARGET_GENES, NFXL1_TARGET_GENES, BARX2_TARGET_GENES, MILI_PSEUDOPODIA_HAPTOTAXIS_DN, BREDEMEYER_RAG_SIGNALING_NOT_VIA_ATM_DN

GO Biological Process (0):

GO Molecular Function (0):

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

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

2 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
KANTR	VIRMA	Q69YN4	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A1W2P7I0, A0A1W2PQU2, A0ZZ18, A4ZUC9, A7M917, A8W3K3, O86220, P0C5R8, P10347, P12163, P12164, P14237, P38452, P41613, P47377, P56782, P87273, Q02268, Q06094, Q06GS7, Q06H14, Q06RE8, Q09MJ5, Q0G9N6, Q0G9X9, Q0ZJ37, Q12111, Q14FH4, Q1KXX6, Q2L8Z0, Q2MIB7, Q2MIK4, Q2PMS6, Q2VEJ3, Q33C56, Q3BAQ9, Q3C1G0, Q49L15, Q4VZQ0, Q56P17

Diamond homologs: A0A1W2P7I0, A0A1W2PQU2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

483 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:53124366:T:C	F32L	0.680
X:53124368:T:A	F32L	0.680
X:53124368:T:G	F32L	0.680
X:53124477:G:A	G69R	0.615
X:53124477:G:C	G69R	0.615

dbSNP variants (sampled 300 via entrez): RS1000071850 (X:53096914 A>C), RS1000216079 (X:53092605 A>G), RS1000310796 (X:53092262 C>A,G,T), RS1000328521 (X:53138502 A>T), RS1000379069 (X:53102224 G>A), RS1000718948 (X:53108148 C>T), RS1000749904 (X:53101779 C>G), RS1001066604 (X:53117591 G>C), RS1001115846 (X:53100255 C>T), RS1001313534 (X:53094044 G>T), RS1001531339 (X:53111976 T>C,G), RS1001686689 (X:53122257 A>G), RS1001790036 (X:53109385 A>G), RS1001800575 (X:53133541 G>A), RS1001906344 (X:53111439 T>C)

Disease associations

OMIM: gene MIM:301019 | 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

4 total (human), top 4 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
triphenyl phosphate	affects expression	1
perfluorooctane sulfonic acid	increases expression	1
Silicon Dioxide	decreases expression	1
Cadmium Chloride	decreases expression	1

Clinical trials (associated diseases)

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