MAP6D1

Summary

MAP6D1 (MAP6 domain containing 1, HGNC:25753) is a protein-coding gene on chromosome 3q27.1, encoding MAP6 domain-containing protein 1 (Q9H9H5). May have microtubule-stabilizing activity.

This gene encodes a protein highly similar to the mouse MAP6 domain containing 1 protein, which is related to the STOP proteins. Based on the study of the mouse protein, the encoded protein may function as a calmodulin-regulated neuronal protein that binds and stabilizes microtubules but also associates with the Golgi membranes through N-terminal palmitoylation.

Source: NCBI Gene 79929 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 25 total — 2 pathogenic
• MANE Select transcript: NM_024871

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:25753
Approved symbol	MAP6D1
Name	MAP6 domain containing 1
Location	3q27.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ12748, SL21
Ensembl gene	ENSG00000180834
Ensembl biotype	protein_coding
OMIM	610593
Entrez	79929

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000318631, ENST00000431348, ENST00000445426, ENST00000463801, ENST00000933005

RefSeq mRNA: 1 — MANE Select: NM_024871 NM_024871

CCDS: CCDS3247

Canonical transcript exons

ENST00000318631 — 3 exons

Exon	Start	End
ENSE00001278346	183817994	183818111
ENSE00001278358	183815922	183817436
ENSE00001627911	183825147	183825577

Expression profiles

Bgee: expression breadth ubiquitous, 131 present calls, max score 96.97.

FANTOM5 (CAGE): breadth broad, TPM avg 2.4383 / max 210.6212, expressed in 424 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
45843	2.0809	406
45842	0.1129	57
45844	0.0755	39
45839	0.0710	32
45841	0.0686	37
45840	0.0295	13

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
C1 segment of cervical spinal cord	UBERON:0006469	96.97	gold quality
cerebellar cortex	UBERON:0002129	96.17	gold quality
cerebellar hemisphere	UBERON:0002245	96.13	gold quality
cerebellum	UBERON:0002037	96.12	gold quality
right hemisphere of cerebellum	UBERON:0014890	96.08	gold quality
substantia nigra	UBERON:0002038	93.37	gold quality
primary visual cortex	UBERON:0002436	93.02	gold quality
Ammon’s horn	UBERON:0001954	92.79	gold quality
corpus callosum	UBERON:0002336	92.44	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.42	gold quality
putamen	UBERON:0001874	92.10	gold quality
right frontal lobe	UBERON:0002810	90.44	gold quality
caudate nucleus	UBERON:0001873	89.81	gold quality
temporal lobe	UBERON:0001871	89.68	gold quality
amygdala	UBERON:0001876	89.64	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	89.28	gold quality
frontal cortex	UBERON:0001870	89.18	gold quality
superior frontal gyrus	UBERON:0002661	89.05	gold quality
cerebral cortex	UBERON:0000956	89.00	gold quality
prefrontal cortex	UBERON:0000451	88.23	gold quality
brain	UBERON:0000955	88.06	gold quality
nucleus accumbens	UBERON:0001882	87.02	gold quality
hypothalamus	UBERON:0001898	86.68	gold quality
anterior cingulate cortex	UBERON:0009835	85.64	gold quality
hindlimb stylopod muscle	UBERON:0004252	84.84	gold quality
gastrocnemius	UBERON:0001388	79.50	gold quality
muscle of leg	UBERON:0001383	79.39	gold quality
cortical plate	UBERON:0005343	78.61	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	78.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	77.15	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.54

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

45 targeting MAP6D1, 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-12118	100.00	65.88	1270
HSA-MIR-6891-5P	99.98	66.53	1372
HSA-MIR-3173-3P	99.98	66.49	1217
HSA-MIR-3658	99.96	73.87	4379
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4492	99.87	68.25	3611
HSA-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-7856-5P	99.75	69.99	2901
HSA-MIR-518A-5P	99.70	69.01	2209
HSA-MIR-527	99.70	69.01	2209
HSA-MIR-548AU-3P	99.70	68.22	1373
HSA-MIR-1251-3P	99.64	67.21	1408
HSA-MIR-4756-3P	99.62	66.30	1319
HSA-MIR-802	99.61	67.70	1254
HSA-MIR-762	99.58	66.61	1994
HSA-MIR-216A-5P	99.50	68.02	1288
HSA-MIR-4498	99.47	67.42	2360
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-6734-3P	99.15	66.27	1627
HSA-MIR-5001-5P	99.05	66.76	1972
HSA-MIR-10524-5P	99.05	66.08	963
HSA-MIR-4738-3P	98.98	67.98	1846
HSA-MIR-154-5P	98.92	66.65	733
HSA-MIR-1304-3P	98.29	66.44	1207
HSA-MIR-3665	97.73	65.08	975

Literature-anchored findings (GeneRIF, showing 1)

• This paper describes the conserved domains, localization and function of the mouse MAP6D1 protein. It also compared the sequences of the related proteins in mouse, human and other species. (PMID:16837464)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	map6d1	ENSDARG00000079777
mus_musculus	Map6d1	ENSMUSG00000041205
rattus_norvegicus	Map6d1	ENSRNOG00000090872

Paralogs (1): MAP6 (ENSG00000171533)

Protein

Protein identifiers

MAP6 domain-containing protein 1 — Q9H9H5 (reviewed: Q9H9H5)

Alternative names: 21 kDa STOP-like protein

All UniProt accessions (3): Q9H9H5, C9JPF8, H7BZQ6

UniProt curated annotations — full annotation on UniProt →

Function. May have microtubule-stabilizing activity.

Subunit / interactions. Interacts with calmodulin.

Subcellular location. Golgi apparatus. Cytoplasm. Cytoskeleton.

Post-translational modifications. Palmitoylated. Palmitoylation enhances association with microtubules.

Similarity. Belongs to the STOP family.

RefSeq proteins (1): NP_079147* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR007882	MAP6	Family

UniProt features (12 total): region of interest 3, mutagenesis site 3, lipid moiety-binding region 3, modified residue 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H9H5-F1	57.09	0.00

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 (5): 38, 167, 5, 10, 11

Mutagenesis-validated functional residues (3):

Position	Phenotype
10	loss of golgi colocalization and gain of microtubule colocalization; when associated with c-5 and c-11.
11	loss of golgi colocalization and gain of microtubule colocalization; when associated with c-5 and c-10.
5	loss of golgi colocalization and gain of microtubule colocalization; when associated with c-10 and c-11.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 93 (showing top): GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_MICROTUBULE_DEPOLYMERIZATION, GOCC_GOLGI_ASSOCIATED_VESICLE, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, GOBP_PROTEIN_DEPOLYMERIZATION, GOBP_REGULATION_OF_MICROTUBULE_POLYMERIZATION_OR_DEPOLYMERIZATION, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_DISASSEMBLY, GOBP_REGULATION_OF_CYTOSKELETON_ORGANIZATION, GOBP_NEGATIVE_REGULATION_OF_ORGANELLE_ORGANIZATION, MODULE_69, GOCC_CIS_GOLGI_NETWORK, GEORGES_TARGETS_OF_MIR192_AND_MIR215, GOMF_CYTOSKELETAL_PROTEIN_BINDING, DUTERTRE_ESTRADIOL_RESPONSE_24HR_UP

GO Biological Process (4): microtubule cytoskeleton organization (GO:0000226), negative regulation of microtubule depolymerization (GO:0007026), cytoskeleton-dependent intracellular transport (GO:0030705), regulation of microtubule cytoskeleton organization (GO:0070507)

GO Molecular Function (2): calmodulin binding (GO:0005516), microtubule binding (GO:0008017)

GO Cellular Component (6): Golgi-associated vesicle (GO:0005798), cis-Golgi network (GO:0005801), microtubule (GO:0005874), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membrane-bounded organelle	2
cytoskeleton organization	1
microtubule-based process	1
microtubule depolymerization	1
negative regulation of microtubule polymerization or depolymerization	1
regulation of microtubule depolymerization	1
negative regulation of protein depolymerization	1
negative regulation of supramolecular fiber organization	1
intracellular transport	1
microtubule cytoskeleton organization	1
regulation of microtubule-based process	1
regulation of cytoskeleton organization	1
protein binding	1
tubulin binding	1
cytoplasmic vesicle	1
Golgi apparatus	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
intracellular anatomical structure	1
cellular anatomical structure	1
cytoplasm	1
endomembrane system	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

704 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
MAP6D1	SAXO1	Q8IYX7	612
MAP6D1	CALM1	P02593	593
MAP6D1	CALML6	Q8TD86	593
MAP6D1	CALML3	P27482	593
MAP6D1	CALML4	Q96GE6	593
MAP6D1	CALML5	Q9NZT1	593
MAP6D1	PAXBP1	Q9Y5B6	501
MAP6D1	COMTD1	Q86VU5	500
MAP6D1	DISP2	A7MBM2	493
MAP6D1	DUS2	Q9NX74	489
MAP6D1	RD3L	P0DJH9	487
MAP6D1	YEATS2	Q9ULM3	476
MAP6D1	TMC4	Q7Z404	474
MAP6D1	COPRS	Q9NQ92	472
MAP6D1	PODXL2	Q9NZ53	468

IntAct

2 interactions, top by confidence:

A	B	Type	Score
APP	ESYT2	psi-mi:“MI:0914”(association)	0.350

BioGRID (2): MAP6D1 (Affinity Capture-RNA), MAP6D1 (Positive Genetic)

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GTJ6, A0A1B0GUX0, A0A3Q1MT14, A0JNL1, A5PJD8, B9EJX3, E1B9R1, E1BNS6, F1MMV1, Q0P591, Q148A4, Q14BB9, Q1JPL0, Q2KJ10, Q2MH31, Q2T9T0, Q2TA11, Q32L72, Q32L77, Q3V0Q6, Q5BN46, Q5PQN4, Q5RBH3, Q5RHU7, Q5SPV6, Q5SVJ3, Q5VTT2, Q5VZQ5, Q66HR9, Q6AYM0, Q7Z5V6, Q8CDU5, Q8N5S3, Q8N865, Q8NA69, Q8NCR6, Q8NEG2, Q95LU0, Q96K30

Diamond homologs: B0S4Q5, O73737, Q0P591, Q14BB9, Q63560, Q7TSJ2, Q96JE9, Q9H9H5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	18
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
1527061	GRCh37/hg19 3q26.33-27.3(chr3:182189525-187212935)	Pathogenic
986761	GRCh37/hg19 3q26.33-27.1(chr3:180834336-183551661)x1	Pathogenic

SpliceAI

587 predictions. Top by Δscore:

Variant	Effect	Δscore
3:183817964:ACACC:A	donor_gain	1.0000
3:183817965:CACCC:C	donor_gain	1.0000
3:183817984:T:TA	donor_gain	1.0000
3:183817968:C:A	donor_gain	0.9900
3:183817989:CTGA:C	donor_loss	0.9900
3:183817992:A:AT	donor_loss	0.9900
3:183817993:CCTGG:C	donor_loss	0.9900
3:183818108:CTGT:C	acceptor_gain	0.9900
3:183818110:GTC:G	acceptor_loss	0.9900
3:183818111:TCT:T	acceptor_loss	0.9900
3:183818112:C:CC	acceptor_gain	0.9900
3:183818112:CTGGA:C	acceptor_loss	0.9900
3:183818113:T:A	acceptor_loss	0.9900
3:183825141:CCATA:C	donor_loss	0.9900
3:183825143:ATACC:A	donor_loss	0.9900
3:183825145:ACC:A	donor_loss	0.9900
3:183825146:CCTG:C	donor_loss	0.9900
3:183825153:G:GT	donor_gain	0.9900
3:183817437:C:CA	acceptor_loss	0.9800
3:183817974:TA:T	donor_gain	0.9800
3:183818024:T:TA	donor_gain	0.9800
3:183818105:TTC:T	acceptor_gain	0.9800
3:183818110:GT:G	acceptor_gain	0.9800
3:183817964:ACAC:A	donor_gain	0.9700
3:183817965:CACC:C	donor_gain	0.9700
3:183818109:TGT:T	acceptor_gain	0.9700
3:183818281:C:CA	donor_gain	0.9700
3:183825146:CCT:C	donor_gain	0.9700
3:183818201:C:A	donor_gain	0.9600
3:183819288:C:CA	donor_gain	0.9600

AlphaMissense

1251 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
3:183825541:A:G	W3R	0.998
3:183825541:A:T	W3R	0.998
3:183825500:C:A	W16C	0.997
3:183825500:C:G	W16C	0.997
3:183825502:A:G	W16R	0.997
3:183825502:A:T	W16R	0.997
3:183825539:C:A	W3C	0.997
3:183825539:C:G	W3C	0.997
3:183825527:G:C	S7R	0.996
3:183825527:G:T	S7R	0.996
3:183825529:T:G	S7R	0.996
3:183825517:A:G	C11R	0.994
3:183818102:G:C	F137L	0.993
3:183818102:G:T	F137L	0.993
3:183818104:A:G	F137L	0.993
3:183825520:A:G	C10R	0.992
3:183825534:C:T	C5Y	0.992
3:183825535:A:G	C5R	0.992
3:183825515:G:C	C11W	0.991
3:183825516:C:T	C11Y	0.991
3:183825531:A:G	I6T	0.991
3:183825531:A:T	I6N	0.991
3:183825519:C:T	C10Y	0.990
3:183825528:C:A	S7I	0.990
3:183825533:A:C	C5W	0.990
3:183825516:C:G	C11S	0.986
3:183825517:A:T	C11S	0.986
3:183825519:C:G	C10S	0.986
3:183825520:A:T	C10S	0.986
3:183825489:T:A	D20V	0.983

dbSNP variants (sampled 300 via entrez): RS1000063034 (3:183818367 G>A,T), RS1000093821 (3:183818213 C>G), RS1000906529 (3:183823150 A>C), RS1001829983 (3:183818734 T>C), RS1002108477 (3:183823927 C>T), RS1002155452 (3:183823528 G>A,C), RS1002285306 (3:183824458 A>C,G), RS1002412538 (3:183819372 G>A), RS1002438618 (3:183819241 G>A), RS1002619722 (3:183824658 G>A), RS1002960158 (3:183816274 T>C), RS1003447025 (3:183820064 C>T), RS1003698777 (3:183826444 G>A), RS1003793959 (3:183825386 G>A), RS1003858019 (3:183819185 C>T)

Disease associations

OMIM: gene MIM:610593 | disease phenotypes: MIM:206900

GenCC curated gene-disease

Mondo (1): anophthalmia/microphthalmia-esophageal atresia syndrome (MONDO:0008799)

Orphanet (1): Anophthalmia/microphthalmia-esophageal atresia syndrome (Orphanet:77298)

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

29 total (human), top 29 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	2
Valproic Acid	affects expression, increases expression	2
bisphenol A	affects cotreatment, increases methylation	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	increases expression	1
benzo(e)pyrene	decreases methylation	1
pentanal	increases expression	1
abrine	decreases expression	1
2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine	increases response to substance, decreases expression	1
jinfukang	affects cotreatment, increases expression	1
NSC 689534	affects binding, decreases expression	1
(+)-JQ1 compound	increases expression	1
Temozolomide	increases expression	1
Sunitinib	increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Cisplatin	affects cotreatment, increases expression	1
Copper	affects binding, decreases expression	1
Estradiol	increases expression	1
Hydrogen Peroxide	affects expression	1
Lead	decreases expression	1
Methapyrilene	decreases methylation	1
Methyl Methanesulfonate	decreases expression	1
Silicon Dioxide	increases expression	1
Smoke	decreases expression	1
Tetrachlorodibenzodioxin	increases expression	1
Tretinoin	increases expression	1
Vitamin E	decreases expression	1
Okadaic Acid	decreases expression	1
S-Nitrosoglutathione	decreases expression	1

Clinical trials (associated diseases)

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