ANKRD42

Summary

ANKRD42 (ankyrin repeat domain 42, HGNC:26752) is a protein-coding gene on chromosome 11q14.1, encoding Ankyrin repeat domain-containing protein 42 (Q8N9B4).

Predicted to enable NF-kappaB binding activity and cyclin-dependent protein serine/threonine kinase inhibitor activity. Predicted to act upstream of or within positive regulation of NF-kappaB transcription factor activity and positive regulation of cytokine production involved in inflammatory response. Predicted to be active in nucleus.

Source: NCBI Gene 338699 — RefSeq curated summary.

At a glance

• GWAS associations: 4
• Clinical variants (ClinVar): 82 total — 1 pathogenic
• MANE Select transcript: NM_001300975

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26752
Approved symbol	ANKRD42
Name	ankyrin repeat domain 42
Location	11q14.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ37874, SARP, PPP1R79
Ensembl gene	ENSG00000137494
Ensembl biotype	protein_coding
OMIM	619778
Entrez	338699

Gene structure

Transcript identifiers

Ensembl transcripts: 11 — 10 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000260047, ENST00000393389, ENST00000393392, ENST00000526731, ENST00000528190, ENST00000528722, ENST00000531815, ENST00000531895, ENST00000533342, ENST00000860470, ENST00000934336

RefSeq mRNA: 6 — MANE Select: NM_001300975 NM_001300972, NM_001300973, NM_001300975, NM_001300976, NM_001300977, NM_182603

CCDS: CCDS73355, CCDS73356, CCDS76457, CCDS76458, CCDS76459, CCDS8265

Canonical transcript exons

ENST00000533342 — 11 exons

Exon	Start	End
ENSE00000989063	83227747	83227872
ENSE00000989074	83240759	83240934
ENSE00000989090	83211295	83211430
ENSE00000995859	83224855	83225055
ENSE00001166944	83236404	83236509
ENSE00001469427	83245498	83245624
ENSE00002164195	83193712	83194728
ENSE00002182501	83247943	83248971
ENSE00003469271	83206058	83206165
ENSE00003509858	83210300	83210419
ENSE00003604151	83198479	83198642

Expression profiles

Bgee: expression breadth ubiquitous, 137 present calls, max score 93.11.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 12.9420 / max 201.6350, expressed in 1788 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116062	12.2414	1787
116064	0.4260	206
116063	0.2746	105

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
thymus	UBERON:0002370	93.11	gold quality
left testis	UBERON:0004533	92.08	gold quality
right testis	UBERON:0004534	91.90	gold quality
testis	UBERON:0000473	91.23	gold quality
calcaneal tendon	UBERON:0003701	89.39	gold quality
right uterine tube	UBERON:0001302	89.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	88.61	gold quality
adrenal tissue	UBERON:0018303	88.06	gold quality
adenohypophysis	UBERON:0002196	85.47	gold quality
superior frontal gyrus	UBERON:0002661	85.31	gold quality
left adrenal gland cortex	UBERON:0035825	85.14	gold quality
left adrenal gland	UBERON:0001234	85.06	gold quality
adrenal gland	UBERON:0002369	84.97	gold quality
right adrenal gland cortex	UBERON:0035827	84.57	gold quality
nucleus accumbens	UBERON:0001882	84.48	gold quality
right adrenal gland	UBERON:0001233	84.41	gold quality
pituitary gland	UBERON:0000007	84.36	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	83.98	gold quality
hypothalamus	UBERON:0001898	83.87	gold quality
Brodmann (1909) area 9	UBERON:0013540	83.72	gold quality
primary visual cortex	UBERON:0002436	83.65	gold quality
prefrontal cortex	UBERON:0000451	83.50	gold quality
anterior cingulate cortex	UBERON:0009835	83.37	gold quality
fallopian tube	UBERON:0003889	83.33	gold quality
cerebral cortex	UBERON:0000956	82.93	gold quality
right coronary artery	UBERON:0001625	82.75	gold quality
stromal cell of endometrium	CL:0002255	82.64	gold quality
frontal cortex	UBERON:0001870	82.57	gold quality
Ammon’s horn	UBERON:0001954	82.40	gold quality
caudate nucleus	UBERON:0001873	82.35	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	5.31
E-MTAB-6386	no	216.15

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

53 targeting ANKRD42, 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-6867-5P	100.00	82.21	3464
HSA-MIR-3925-3P	100.00	69.95	1237
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-4789-3P	99.99	70.75	2484
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-3682-5P	99.93	67.97	1163
HSA-MIR-4760-3P	99.93	70.50	2385
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-5195-3P	99.92	70.92	1877
HSA-MIR-3529-3P	99.90	73.55	3045
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-3121-3P	99.82	71.96	3630
HSA-MIR-448	99.79	72.37	2103
HSA-MIR-3913-5P	99.78	67.26	968
HSA-MIR-4319	99.76	69.83	2586
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-12129	99.72	67.45	1311
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-670-5P	99.67	69.94	1565
HSA-MIR-466	99.67	70.85	2863
HSA-MIR-548U	99.65	67.78	1463
HSA-MIR-2113	99.58	71.22	1521
HSA-MIR-3122	99.50	66.33	821
HSA-MIR-140-5P	99.44	67.20	792

Literature-anchored findings (GeneRIF, showing 2)

• the cloning and characterization of a new protein, termed SARP (several ankyrin repeat protein), which is shown to interact with all isoforms of PP1 by a variety of techniques. (PMID:17123353)
• Genome-wide CRISPR screening identifies the pivotal role of ANKRD42 in colorectal cancer metastasis through EMT regulation. (PMID:38822625)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ankrd42	ENSMUSG00000041343
rattus_norvegicus	Ankrd42	ENSRNOG00000009664

Paralogs (1): ANKRD37 (ENSG00000186352)

Protein

Protein identifiers

Ankyrin repeat domain-containing protein 42 — Q8N9B4 (reviewed: Q8N9B4)

All UniProt accessions (7): Q8N9B4, E9PIL2, E9PKE2, E9PP91, E9PR10, F8W6I9, H0YE80

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N9B4-1	1	yes
Q8N9B4-2	2

RefSeq proteins (6): NP_001287901, NP_001287902, NP_001287904, NP_001287905, NP_001287906, NP_872409 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002110	Ankyrin_rpt	Repeat
IPR018247	EF_Hand_1_Ca_BS	Binding_site
IPR036770	Ankyrin_rpt-contain_sf	Homologous_superfamily
IPR050776	Ank_Repeat/CDKN_Inhibitor	Family

Pfam: PF12796

UniProt features (17 total): repeat 9, splice variant 3, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9B4-F1	77.41	0.52

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 98 (showing top): GCANCTGNY_MYOD_Q6, TGGAAA_NFAT_Q4_01, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_DN, GOMF_CYCLIN_DEPENDENT_PROTEIN_SERINE_THREONINE_KINASE_INHIBITOR_ACTIVITY, GOMF_NF_KAPPAB_BINDING, GOMF_PROTEIN_SERINE_THREONINE_KINASE_INHIBITOR_ACTIVITY, GOMF_ENZYME_INHIBITOR_ACTIVITY, GOMF_TRANSCRIPTION_FACTOR_BINDING, GOMF_ENZYME_REGULATOR_ACTIVITY, GOMF_RNA_POLYMERASE_II_SPECIFIC_DNA_BINDING_TRANSCRIPTION_FACTOR_BINDING, GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_BINDING, ELF2_TARGET_GENES, FOXJ2_TARGET_GENES, FOXN3_TARGET_GENES, NFE2L1_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (3): cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861), NF-kappaB binding (GO:0051059), protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cyclin-dependent protein serine/threonine kinase activity	1
cyclin-dependent protein serine/threonine kinase regulator activity	1
protein serine/threonine kinase inhibitor activity	1
RNA polymerase II-specific DNA-binding transcription factor binding	1
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

916 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
ANKRD42	SFRP5	Q5T4F7	834
ANKRD42	SFRP2	Q96HF1	785
ANKRD42	SFRP1	Q8N474	685
ANKRD42	FRZB	Q92765	650
ANKRD42	CCDC90B	Q9GZT6	534
ANKRD42	RAB30	Q15771	480
ANKRD42	HSDL2	Q6YN16	447
ANKRD42	BOLA1	Q9Y3E2	445
ANKRD42	PCF11	O94913	426
ANKRD42	SGTB	Q96EQ0	421
ANKRD42	SRRD	Q9UH36	415
ANKRD42	NOB1	Q9ULX3	415
ANKRD42	ZCCHC14	Q8WYQ9	377
ANKRD42	APOBR	Q0VD83	376
ANKRD42	PACRGL	Q8N7B6	373

IntAct

3 interactions, top by confidence:

A	B	Type	Score
H3C1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.410
JUN	TPM3	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): ANKRD42 (Proximity Label-MS), ANKRD42 (Proximity Label-MS), ANKRD42 (Affinity Capture-MS), ANKRD42 (Cross-Linking-MS (XL-MS)), ANKRD42 (Two-hybrid)

ESM2 similar proteins: A6NK59, A7MB89, B4E2M5, P0C6P7, P0C927, Q08DV6, Q29RM5, Q3SX45, Q3SZE4, Q3UMR0, Q495B1, Q4V890, Q5R5S1, Q5REW9, Q5RFS1, Q5U2S6, Q5ZM55, Q6GPE5, Q7T3P8, Q810B6, Q8C0T1, Q8C6Y6, Q8CEF1, Q8CEL2, Q8HXA6, Q8K0L0, Q8N9B4, Q8VHS6, Q8WXH4, Q8WXK1, Q91ZT8, Q96DX5, Q96JP0, Q96NW4, Q96Q27, Q9BSK4, Q9CQ31, Q9GKW8, Q9H0C1, Q9P2R3

Diamond homologs: B0G124, O95271, Q337A0, Q3V096, Q4JHE0, Q55FM5, Q6PFX9, Q86WC6, Q876A6, Q8N9B4, Q9D119, Q9J512, A4II29, O15084, P25799, Q04749, Q505D1, Q5U5A6, Q63369, Q7T3X9, Q7T3Y0, Q7Z6K4, Q91974, Q91ZA8, Q9C6C3, Q9SMX5, A0A0R4IQZ2, A7MB89, O43150, Q00653, Q0VC93, Q10728, Q28FJ2, Q2T9K6, Q569N2, Q5U464, Q6JAN1, Q6RI86, Q7SIG6, Q7XUW4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	76
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
59771	GRCh38/hg38 11q14.1-14.2(chr11:78362208-86165380)x3	Pathogenic

SpliceAI

1890 predictions. Top by Δscore:

Variant	Effect	Δscore
11:83210292:A:AG	acceptor_gain	1.0000
11:83210293:T:G	acceptor_gain	1.0000
11:83210297:TA:T	acceptor_loss	1.0000
11:83210298:A:AC	acceptor_loss	1.0000
11:83210298:A:AG	acceptor_gain	1.0000
11:83210298:AG:A	acceptor_gain	1.0000
11:83210299:G:A	acceptor_gain	1.0000
11:83210299:G:GA	acceptor_gain	1.0000
11:83210299:GGC:G	acceptor_gain	1.0000
11:83210299:GGCT:G	acceptor_gain	1.0000
11:83210299:GGCTC:G	acceptor_gain	1.0000
11:83210415:GAGTG:G	donor_gain	1.0000
11:83210417:GTG:G	donor_gain	1.0000
11:83210418:TG:T	donor_gain	1.0000
11:83210419:GG:G	donor_gain	1.0000
11:83210419:GGT:G	donor_loss	1.0000
11:83210420:G:GG	donor_gain	1.0000
11:83210421:T:A	donor_loss	1.0000
11:83211426:TCCAG:T	donor_loss	1.0000
11:83211427:CCAG:C	donor_loss	1.0000
11:83211428:CAGGT:C	donor_loss	1.0000
11:83211429:AG:A	donor_loss	1.0000
11:83211430:GGTAT:G	donor_loss	1.0000
11:83211431:G:A	donor_loss	1.0000
11:83211432:T:A	donor_loss	1.0000
11:83224853:A:AG	acceptor_gain	1.0000
11:83224854:G:GA	acceptor_gain	1.0000
11:83224854:GTT:G	acceptor_gain	1.0000
11:83224854:GTTC:G	acceptor_gain	1.0000
11:83224854:GTTCA:G	acceptor_gain	1.0000

AlphaMissense

3503 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:83211364:T:C	C146R	0.991
11:83211366:C:G	C146W	0.991
11:83211356:G:C	R143P	0.990
11:83206136:G:C	A73P	0.989
11:83206134:C:A	A72D	0.988
11:83224867:C:A	A172D	0.988
11:83224889:T:G	C179W	0.988
11:83210367:C:A	A105D	0.987
11:83211341:C:A	A138E	0.987
11:83224866:G:C	A172P	0.987
11:83236406:G:C	A278P	0.986
11:83210369:G:C	A106P	0.983
11:83211344:C:A	A139D	0.983
11:83236407:C:A	A278D	0.983
11:83206133:G:C	A72P	0.982
11:83206137:C:A	A73E	0.982
11:83211343:G:C	A139P	0.982
11:83211374:T:C	L149P	0.982
11:83210364:T:C	L104P	0.981
11:83210366:G:C	A105P	0.981
11:83210370:C:A	A106E	0.981
11:83224887:T:C	C179R	0.981
11:83210379:G:T	G109V	0.980
11:83211352:G:T	G142W	0.980
11:83211353:G:T	G142V	0.980
11:83211428:C:G	P167R	0.980
11:83224864:C:A	A171E	0.979
11:83227872:G:C	A277P	0.979
11:83210304:T:C	L84P	0.977
11:83210379:G:A	G109E	0.977

dbSNP variants (sampled 300 via entrez): RS1000008295 (11:83229950 A>G), RS1000169445 (11:83207771 A>G), RS1000224081 (11:83248585 C>G,T), RS1000248036 (11:83255824 C>G,T), RS1000267114 (11:83213328 G>A,T), RS1000292165 (11:83229827 G>T), RS1000389203 (11:83255396 AAAAC>A), RS1000403170 (11:83235977 T>G), RS1000461109 (11:83201625 TAA>T), RS1000465480 (11:83195956 C>A,T), RS1000573584 (11:83201979 A>G,T), RS1000597962 (11:83214366 A>G,T), RS1000606941 (11:83243216 T>C), RS1000633991 (11:83214140 C>T), RS1000736718 (11:83250572 A>G)

Disease associations

OMIM: gene MIM:619778 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

4 associations (top):

Study	Trait	p-value
GCST010002_244	Refractive error	2.000000e-53
GCST010135_38	Oily fish consumption	9.000000e-09
GCST010140_28	Pork consumption	9.000000e-09
GCST010703_247	Brain morphology (MOSTest)	2.000000e-14

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0008111	diet measurement
EFO:0004346	neuroimaging 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	affects cotreatment, increases abundance, increases expression	2
Arsenic	affects methylation, affects cotreatment, increases abundance, increases expression	2
GSK-J4	decreases expression	1
bisphenol A	increases expression	1
2-methyl-4-isothiazolin-3-one	increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
benzo(e)pyrene	increases methylation	1
pentanal	decreases expression	1
Sunitinib	decreases expression	1
Vorinostat	decreases expression	1
Air Pollutants	increases abundance, affects expression	1
Benzo(a)pyrene	affects methylation	1
Gallic Acid	decreases expression	1
Manganese	affects cotreatment, increases abundance, increases expression	1
Methapyrilene	increases methylation	1
Ozone	affects expression, increases abundance	1
Thiram	increases expression	1
Tobacco Smoke Pollution	increases expression	1
Tretinoin	increases expression	1
Urethane	increases expression	1
Aflatoxin B1	increases methylation	1
Cadmium Chloride	decreases expression	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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