SLC4A1AP

Summary

SLC4A1AP (solute carrier family 4 member 1 adaptor protein, HGNC:13813) is a protein-coding gene on chromosome 2p23.3, encoding Kanadaptin (Q9BWU0).

Predicted to enable mRNA binding activity. Located in nucleoplasm and plasma membrane.

Source: NCBI Gene 22950 — RefSeq curated summary.

At a glance

• GWAS associations: 6
• Clinical variants (ClinVar): 117 total
• MANE Select transcript: NM_018158

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13813
Approved symbol	SLC4A1AP
Name	solute carrier family 4 member 1 adaptor protein
Location	2p23.3
Locus type	gene with protein product
Status	Approved
Aliases	kanadaptin, HLC3
Ensembl gene	ENSG00000163798
Ensembl biotype	protein_coding
OMIM	602655
Entrez	22950

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 10 protein_coding, 4 nonsense_mediated_decay, 1 retained_intron

ENST00000326019, ENST00000427424, ENST00000492196, ENST00000613517, ENST00000618046, ENST00000696011, ENST00000696012, ENST00000696013, ENST00000696014, ENST00000696015, ENST00000901631, ENST00000901632, ENST00000912953, ENST00000912954, ENST00000953679

RefSeq mRNA: 1 — MANE Select: NM_018158 NM_018158

CCDS: CCDS33166

Canonical transcript exons

ENST00000326019 — 14 exons

Exon	Start	End
ENSE00001178825	27693685	27693754
ENSE00001687098	27663889	27664577
ENSE00001902277	27694634	27694969
ENSE00003965762	27677295	27677364
ENSE00003965763	27667268	27667390
ENSE00003965764	27675532	27675692
ENSE00003965769	27682248	27682359
ENSE00003965772	27687934	27688020
ENSE00003965773	27688700	27688767
ENSE00003965775	27677738	27677924
ENSE00003965778	27685037	27685277
ENSE00003965784	27665100	27665295
ENSE00003965787	27668843	27668903
ENSE00003965788	27669248	27669387

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 93.50.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 20.1374 / max 1035.1434, expressed in 1809 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
19395	18.1927	1806
19396	0.6301	247
19392	0.4773	220
19391	0.3412	112
19389	0.3333	119
19390	0.1627	31

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	93.50	gold quality
quadriceps femoris	UBERON:0001377	92.50	gold quality
corpus callosum	UBERON:0002336	92.34	gold quality
prefrontal cortex	UBERON:0000451	90.94	gold quality
superior frontal gyrus	UBERON:0002661	90.75	gold quality
frontal cortex	UBERON:0001870	90.50	gold quality
Brodmann (1909) area 9	UBERON:0013540	90.38	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	90.34	gold quality
cerebellar vermis	UBERON:0004720	90.21	gold quality
cerebellar cortex	UBERON:0002129	90.10	gold quality
cerebellar hemisphere	UBERON:0002245	90.09	gold quality
gastrocnemius	UBERON:0001388	90.05	gold quality
muscle of leg	UBERON:0001383	90.02	gold quality
cerebellum	UBERON:0002037	90.02	gold quality
testis	UBERON:0000473	89.87	gold quality
right testis	UBERON:0004534	89.80	gold quality
right frontal lobe	UBERON:0002810	89.76	gold quality
left testis	UBERON:0004533	89.69	gold quality
cerebral cortex	UBERON:0000956	89.68	gold quality
sural nerve	UBERON:0015488	89.60	gold quality
skeletal muscle tissue	UBERON:0001134	89.59	gold quality
monocyte	CL:0000576	89.51	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	89.49	gold quality
right hemisphere of cerebellum	UBERON:0014890	89.38	gold quality
leukocyte	CL:0000738	89.28	gold quality
anterior cingulate cortex	UBERON:0009835	89.13	gold quality
primary visual cortex	UBERON:0002436	89.01	gold quality
islet of Langerhans	UBERON:0000006	88.95	gold quality
muscle tissue	UBERON:0002385	88.68	gold quality
brain	UBERON:0000955	88.66	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.74
E-MTAB-7303	no	530.37
E-MTAB-7381	no	212.09

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

28 targeting SLC4A1AP, 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-371B-5P	99.99	75.34	4759
HSA-MIR-520D-5P	99.98	73.34	4883
HSA-MIR-524-5P	99.98	73.43	4882
HSA-MIR-4803	99.98	71.99	3117
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-204-5P	99.79	71.62	2439
HSA-MIR-211-5P	99.79	71.65	2440
HSA-MIR-200A-5P	99.76	69.10	949
HSA-MIR-200B-5P	99.76	69.05	948
HSA-MIR-105-5P	99.54	69.24	2060
HSA-MIR-7853-5P	99.54	69.30	2055
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-671-5P	99.52	67.11	1277
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-514B-5P	99.50	68.19	1766
HSA-MIR-5571-5P	99.49	66.99	1764
HSA-MIR-6513-5P	99.43	67.81	1071
HSA-MIR-4786-3P	99.36	68.35	1390
HSA-MIR-3191-5P	99.24	66.52	1722
HSA-MIR-3190-5P	98.87	64.89	1345
HSA-MIR-6895-3P	98.79	65.69	996
HSA-MIR-12125	98.59	67.54	1044
HSA-MIR-1248	98.47	67.54	1314
HSA-MIR-4733-3P	98.35	65.20	994
HSA-MIR-15B-3P	97.85	66.68	974
HSA-MIR-4733-5P	97.75	67.44	866
HSA-MIR-1226-3P	97.51	66.32	1063

Literature-anchored findings (GeneRIF, showing 2)

• human kanadaptin did not interact with kidney anion exchanger 1 (kAE1) and had no effect on trafficking of kAE1 to the plasma membrane (PMID:15764369)
• Structural insights into the recognition of phosphopeptide by the FHA domain of kanadaptin (PMID:25197798)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	slc4a1ap	ENSDARG00000034160
mus_musculus	Slc4a1ap	ENSMUSG00000029141
rattus_norvegicus	Slc4a1ap	ENSRNOG00000004901
caenorhabditis_elegans		WBGENE00014011

Paralogs (2): PPP1R8 (ENSG00000117751), SNIP1 (ENSG00000163877)

Protein

Protein identifiers

Kanadaptin — Q9BWU0 (reviewed: Q9BWU0)

Alternative names: Human lung cancer oncogene 3 protein, Kidney anion exchanger adapter protein, Solute carrier family 4 anion exchanger member 1 adapter protein

All UniProt accessions (7): A0A087WWF4, A0A8Q3WKX1, A0A8Q3WKX3, A0A8Q3WKX9, A0A8Q3WLG9, Q9BWU0, H7C256

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus. Cytoplasm.

Tissue specificity. Ubiquitously expressed.

Miscellaneous. Isoform 2 is a prediction based on conservation with orthologs.

Isoforms (2)

UniProt ID	Names	Canonical?
Q9BWU0-2	2	yes
Q9BWU0-1	1

RefSeq proteins (1): NP_060628* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000253	FHA_dom	Domain
IPR008984	SMAD_FHA_dom_sf	Homologous_superfamily
IPR014720	dsRBD_dom	Domain
IPR050923	Cell_Proc_Reg/RNA_Proc	Family

Pfam: PF00035, PF00498

UniProt features (40 total): compositionally biased region 9, strand 9, modified residue 7, sequence conflict 5, region of interest 3, sequence variant 2, chain 1, domain 1, cross-link 1, splice variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

1 structures.

PDB	Method	Resolution (Å)
4H87	X-RAY DIFFRACTION	1.55

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BWU0-F1	64.55	0.23

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (8): 28, 90, 258, 412, 476, 655, 658, 441

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_DN, WANG_LMO4_TARGETS_DN, MILI_PSEUDOPODIA_HAPTOTAXIS_UP, LASTOWSKA_COAMPLIFIED_WITH_MYCN, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_UP, RYTTCCTG_ETS2_B, MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN, ACEVEDO_LIVER_CANCER_UP, WANG_PROSTATE_CANCER_ANDROGEN_INDEPENDENT, BENPORATH_OCT4_TARGETS, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOMF_MRNA_BINDING, HAMAI_APOPTOSIS_VIA_TRAIL_UP, BRUINS_UVC_RESPONSE_EARLY_LATE, MTOR_UP.N4.V1_UP

GO Biological Process (0):

GO Molecular Function (2): mRNA binding (GO:0003729), protein binding (GO:0005515)

GO Cellular Component (4): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), plasma membrane (GO:0005886), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
RNA binding	1
binding	1
nuclear lumen	1
intracellular anatomical structure	1
membrane	1
cell periphery	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

974 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
SLC4A1AP	OSGEP	Q9NPF4	943
SLC4A1AP	SLC4A1	P02730	749
SLC4A1AP	SPATA31H1	Q68DN1	543
SLC4A1AP	AMMECR1L	Q6DCA0	525
SLC4A1AP	CCDC121	Q6ZUS5	515
SLC4A1AP	NOL7	Q9UMY1	487
SLC4A1AP	PRPF38A	Q8NAV1	483
SLC4A1AP	ANK2	Q01484	479
SLC4A1AP	ANK1	P16157	471
SLC4A1AP	RBM45	Q8IUH3	471
SLC4A1AP	FCF1	Q9Y324	466
SLC4A1AP	EIF2B4	Q9UI10	465
SLC4A1AP	ZKSCAN5	Q9Y2L8	460
SLC4A1AP	TMUB2	Q71RG4	455
SLC4A1AP	ANK3	Q12955	450

IntAct

102 interactions, top by confidence:

A	B	Type	Score
SNRPF	GEMIN2	psi-mi:“MI:0914”(association)	0.910
CDK8	MED19	psi-mi:“MI:2364”(proximity)	0.850
SNRPE	GEMIN2	psi-mi:“MI:0914”(association)	0.770
RBM11	ZCCHC8	psi-mi:“MI:0914”(association)	0.740
PHF5A	SF3B1	psi-mi:“MI:0914”(association)	0.730
SNRPD2	GEMIN2	psi-mi:“MI:0914”(association)	0.710
SNRPG	GEMIN2	psi-mi:“MI:0914”(association)	0.710
ILK	PXN	psi-mi:“MI:0915”(physical association)	0.670
SNRPB	PRMT5	psi-mi:“MI:0914”(association)	0.670
SNRPA1	HTATSF1	psi-mi:“MI:0914”(association)	0.640
ATXN7L3	USP27X	psi-mi:“MI:0914”(association)	0.640
DNAJC8	SF3B1	psi-mi:“MI:0914”(association)	0.640
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
SNRPA1	U2SURP	psi-mi:“MI:0914”(association)	0.640
SF3B4	SF3B1	psi-mi:“MI:0914”(association)	0.610
SLC4A1AP	ILK	psi-mi:“MI:0915”(physical association)	0.600
ILK	SLC4A1AP	psi-mi:“MI:0915”(physical association)	0.600
SLC4A1AP	ILK	psi-mi:“MI:0403”(colocalization)	0.600
PPP4R2	SF3B1	psi-mi:“MI:0914”(association)	0.570
PPP4R2	SF3B1	psi-mi:“MI:2364”(proximity)	0.570
TCF4	SLC4A1AP	psi-mi:“MI:0915”(physical association)	0.560
SLC4A1AP	TCF4	psi-mi:“MI:0915”(physical association)	0.560

BioGRID (169): SLC4A1AP (Two-hybrid), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), DCLK1 (Co-fractionation), SLC4A1AP (Co-fractionation), TPM2 (Co-fractionation), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Proximity Label-MS), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Affinity Capture-MS), SLC4A1AP (Two-hybrid)

ESM2 similar proteins: A0JNI5, A2AQ19, D3ZTQ1, O43290, O43395, P21675, P35269, P49140, Q02614, Q12872, Q13435, Q2KIA6, Q2KIT1, Q3THK3, Q3TIV5, Q3U155, Q3UJB0, Q3USH5, Q53F19, Q5EA53, Q5HZB6, Q5R5F1, Q5R5J3, Q5RAD5, Q5U3K5, Q5XIW8, Q5ZIH9, Q5ZJ85, Q5ZM19, Q60544, Q6AY96, Q6PII3, Q6U6G5, Q75QI0, Q80UV9, Q8BVA4, Q8BZR9, Q8CFC7, Q8N2M8, Q8WU90

Diamond homologs: A0JM08, Q498L0, Q5M9G6, Q5SW79, Q6A065, Q80U49, Q8BIZ6, Q8TAD8, Q96L14, Q9BWU0, Q9Y4F5, A0QNG6, A0QYG2, P64898, P9WJA8, P9WJA9, P9WJB4, P9WJB5, Q10322, Q4JVU0, Q6NHD4, Q8FTJ5, Q8NQJ3, B7SY83, Q12972, Q28147, Q8R3G1, Q9FIK2, P34648, Q54VU4, Q07930, Q8W4D8, B1AJZ9

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 96 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Metabolism of non-coding RNA	6	51.4×	5e-08
mRNA Splicing - Minor Pathway	13	39.3×	2e-16
mRNA Polyadenylation	24	28.5×	6e-27
mRNA Splicing	19	28.2×	5e-21
CHD1 and CHD2 subfamily	18	26.5×	2e-19
Processing of Capped Intron-Containing Pre-mRNA	21	23.3×	2e-21
SARS-CoV-2 modulates host translation machinery	7	21.2×	1e-06
mRNA Splicing - Major Pathway	28	20.7×	1e-27

GO biological processes:

GO term	Partners	Fold	FDR
U2-type prespliceosome assembly	15	102.9×	1e-25
regulation of mRNA splicing, via spliceosome	6	58.5×	4e-08
RNA splicing, via transesterification reactions	7	48.0×	1e-08
spliceosomal complex assembly	7	46.3×	1e-08
spliceosomal snRNP assembly	7	44.7×	1e-08
mRNA splicing, via spliceosome	25	25.2×	8e-26
RNA splicing	23	22.3×	9e-23
regulation of DNA repair	6	18.2×	5e-05

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	98
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1925 predictions. Top by Δscore:

Variant	Effect	Δscore
2:27664574:GCAG:G	donor_gain	1.0000
2:27664578:G:C	donor_loss	1.0000
2:27665089:T:TA	acceptor_gain	1.0000
2:27665098:A:AG	acceptor_gain	1.0000
2:27665098:A:T	acceptor_loss	1.0000
2:27665098:AGG:A	acceptor_gain	1.0000
2:27665099:G:GG	acceptor_gain	1.0000
2:27665099:GGG:G	acceptor_gain	1.0000
2:27665223:G:GT	donor_gain	1.0000
2:27665243:GAAGA:G	donor_gain	1.0000
2:27665247:A:G	donor_gain	1.0000
2:27665274:A:G	donor_gain	1.0000
2:27665294:GG:G	donor_gain	1.0000
2:27665294:GGGTA:G	donor_loss	1.0000
2:27665295:GG:G	donor_gain	1.0000
2:27665296:G:GG	donor_gain	1.0000
2:27665296:GT:G	donor_loss	1.0000
2:27665297:T:G	donor_loss	1.0000
2:27667257:A:AG	acceptor_gain	1.0000
2:27667258:T:G	acceptor_gain	1.0000
2:27667259:A:AG	acceptor_gain	1.0000
2:27667259:ATCCT:A	acceptor_gain	1.0000
2:27667260:T:G	acceptor_gain	1.0000
2:27667263:T:A	acceptor_gain	1.0000
2:27667263:TGTA:T	acceptor_loss	1.0000
2:27667264:GTAGG:G	acceptor_loss	1.0000
2:27667265:TAG:T	acceptor_loss	1.0000
2:27667265:TAGGA:T	acceptor_gain	1.0000
2:27667266:A:AG	acceptor_gain	1.0000
2:27667266:A:T	acceptor_loss	1.0000

AlphaMissense

5212 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:27667385:G:C	R380P	1.000
2:27669250:T:C	L403S	1.000
2:27669286:C:A	A415D	1.000
2:27669332:C:G	C430W	1.000
2:27669345:T:C	C435R	1.000
2:27669347:T:G	C435W	1.000
2:27669355:T:A	L438H	1.000
2:27669355:T:C	L438P	1.000
2:27693739:T:A	W776R	1.000
2:27693739:T:C	W776R	1.000
2:27667367:T:A	L374H	0.999
2:27667367:T:C	L374P	0.999
2:27667375:T:C	F377L	0.999
2:27667377:T:A	F377L	0.999
2:27667377:T:G	F377L	0.999
2:27668893:T:C	C399R	0.999
2:27668894:G:A	C399Y	0.999
2:27668895:C:G	C399W	0.999
2:27669318:G:C	A426P	0.999
2:27669330:T:C	C430R	0.999
2:27669331:G:A	C430Y	0.999
2:27669342:G:C	A434P	0.999
2:27669343:C:A	A434D	0.999
2:27669346:G:A	C435Y	0.999
2:27669349:G:C	R436P	0.999
2:27675591:G:C	D469H	0.999
2:27675641:A:C	R485S	0.999
2:27675641:A:T	R485S	0.999
2:27677873:T:C	L571P	0.999
2:27693741:G:C	W776C	0.999

dbSNP variants (sampled 300 via entrez): RS1000045824 (2:27681781 C>G), RS1000103681 (2:27689211 C>T), RS1000322375 (2:27673212 T>C,G), RS1000382792 (2:27674299 A>G), RS1000437089 (2:27673003 A>C,G), RS1000459256 (2:27695308 T>C), RS1000550005 (2:27680042 CAT>C), RS1000558450 (2:27687072 G>A), RS1000573483 (2:27694949 A>G), RS1000724981 (2:27686923 T>C), RS1000769521 (2:27668216 T>C), RS1000932746 (2:27680075 C>A,T), RS1001047324 (2:27679891 A>T), RS1001118216 (2:27687391 T>C), RS1001319446 (2:27693027 C>T)

Disease associations

OMIM: gene MIM:602655 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

6 associations (top):

Study	Trait	p-value
GCST001342_1	Alzheimer’s disease	2.000000e-06
GCST001585_26	Breast size	1.000000e-06
GCST001585_6	Breast size	5.000000e-06
GCST003048_130	Schizophrenia	4.000000e-08
GCST008103_38	Bipolar disorder	1.000000e-07
GCST010107_7	L-selectin levels	5.000000e-06

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0008202	L-Selectin measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

24 total (human), top 24 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases abundance, increases expression	2
Cyclosporine	increases expression	2
aristolochic acid I	increases expression	1
FR900359	affects phosphorylation	1
deoxynivalenol	increases expression	1
beta-lapachone	decreases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
coumarin	decreases phosphorylation	1
abrine	increases expression	1
Acetaminophen	decreases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases abundance, increases expression	1
Atrazine	increases expression	1
Enzyme Inhibitors	decreases activity, increases O-linked glycosylation	1
Gallic Acid	increases expression	1
Ivermectin	decreases expression	1
Lead	increases expression	1
Methyl Methanesulfonate	increases expression	1
Mustard Gas	increases phosphorylation	1
Rotenone	decreases expression	1
Valproic Acid	increases expression	1
Cadmium Chloride	decreases expression	1
Palmitic Acid	decreases phosphorylation	1
Particulate Matter	decreases expression, increases abundance	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_TN89	HAP1 SLC4A1AP (-)	Cancer cell line	Male

Clinical trials (associated diseases)

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