GOLGA6L2

Summary

GOLGA6L2 (golgin A6 family like 2, HGNC:26695) is a protein-coding gene on chromosome 15q11.2, encoding Golgin subfamily A member 6-like protein 2 (Q8N9W4).

Predicted to be located in cis-Golgi network.

Source: NCBI Gene 283685 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 24 total — 11 pathogenic, 1 likely-pathogenic
• MANE Select transcript: NM_001304388

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26695
Approved symbol	GOLGA6L2
Name	golgin A6 family like 2
Location	15q11.2
Locus type	gene with protein product
Status	Approved
Aliases	CT105, FLJ36144
Ensembl gene	ENSG00000174450
Ensembl biotype	protein_coding
Entrez	283685

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 1 nonsense_mediated_decay, 1 protein_coding

ENST00000566571, ENST00000567107

RefSeq mRNA: 1 — MANE Select: NM_001304388 NM_001304388

CCDS: CCDS76728

Canonical transcript exons

ENST00000567107 — 8 exons

Exon	Start	End
ENSE00001273187	23444471	23444500
ENSE00001786789	23441979	23442120
ENSE00003466772	23439038	23441682
ENSE00003471143	23445310	23445438
ENSE00003512641	23444162	23444212
ENSE00003584508	23442450	23442508
ENSE00003680662	23443777	23444073
ENSE00003894767	23447098	23447243

Expression profiles

Bgee: expression breadth broad, 18 present calls, max score 91.28.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0360 / max 36.5379, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
148990	0.0360	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	91.28	gold quality
right testis	UBERON:0004534	91.13	gold quality
testis	UBERON:0000473	90.11	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.02	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	63.33	silver quality
stromal cell of endometrium	CL:0002255	52.68	silver quality
ganglionic eminence	UBERON:0004023	48.21	silver quality
gall bladder	UBERON:0002110	41.04	gold quality
bone marrow	UBERON:0002371	40.31	gold quality
skeletal muscle tissue	UBERON:0001134	40.19	gold quality
cortical plate	UBERON:0005343	39.93	gold quality
monocyte	CL:0000576	39.91	gold quality
lymph node	UBERON:0000029	39.28	gold quality
leukocyte	CL:0000738	38.80	gold quality
right adrenal gland cortex	UBERON:0035827	38.73	silver quality
lower esophagus mucosa	UBERON:0035834	38.27	gold quality
bone marrow cell	CL:0002092	38.20	gold quality
superior frontal gyrus	UBERON:0002661	37.98	gold quality
left adrenal gland	UBERON:0001234	37.61	silver quality
muscle tissue	UBERON:0002385	37.28	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
adrenal gland	UBERON:0002369	36.33	silver quality
left adrenal gland cortex	UBERON:0035825	36.32	gold quality
urinary bladder	UBERON:0001255	36.11	silver quality
hindlimb stylopod muscle	UBERON:0004252	35.71	gold quality
liver	UBERON:0002107	35.62	gold quality
mucosa of transverse colon	UBERON:0004991	35.18	gold quality
right coronary artery	UBERON:0001625	35.14	gold quality
muscle of leg	UBERON:0001383	33.49	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.12

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (10): GOLGA6L4 (ENSG00000184206), GOLGA6L9 (ENSG00000197978), GOLGA6L25 (ENSG00000227717), GOLGA6L24 (ENSG00000237850), GOLGA6L7 (ENSG00000261649), GOLGA6L26 (ENSG00000273756), GOLGA6L1 (ENSG00000273976), GOLGA6L6 (ENSG00000277322), GOLGA6L22 (ENSG00000277865), GOLGA6L10 (ENSG00000278662)

Protein

Protein identifiers

Golgin subfamily A member 6-like protein 2 — Q8N9W4 (reviewed: Q8N9W4)

All UniProt accessions (2): Q8N9W4, H3BS38

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the GOLGA6 family.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8N9W4-3	3	yes
Q8N9W4-1	1
Q8N9W4-2	2

RefSeq proteins (1): NP_001291317* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026737	GOLGA6L	Family

UniProt features (35 total): compositionally biased region 14, region of interest 5, splice variant 5, sequence variant 5, sequence conflict 4, chain 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N9W4-F1	62.54	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): chr15q11, TGIF_01, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, MIR559, MIR548Y, MIR548BB_5P, MIR548AR_5P, MIR548AD_5P_MIR548AE_5P_MIR548AY_5P_MIR548B_5P_MIR548D_5P, MIR548AK_MIR548AM_5P_MIR548C_5P_MIR548H_5P_MIR548O_5P_MIR548AU_5P, MIR548O_5P_MIR548W, MIR548AB, MIR548AS_5P, MIR548A_5P, MIR548AQ_5P, MIR548I

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

422 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
GOLGA6L2	TEX55	Q96M34	506
GOLGA6L2	NUF2	Q9BZD4	504
GOLGA6L2	FAM186A	A6NE01	448
GOLGA6L2	OR4L1	Q8NH43	445
GOLGA6L2	FER1L6	Q2WGJ9	419
GOLGA6L2	MFSD6L	Q8IWD5	390
GOLGA6L2	WDR89	Q96FK6	380
GOLGA6L2	TMEM247	A6NEH6	378
GOLGA6L2	APP	P05067	373
GOLGA6L2	OR4C5	Q8NGB2	370
GOLGA6L2	OR51A2	Q8NGJ7	369
GOLGA6L2	DCDC2B	A2VCK2	366
GOLGA6L2	MUC4	Q99102	348
GOLGA6L2	GLIPR1L1	Q6UWM5	322
GOLGA6L2	M0QY95	M0QY95	322

IntAct

8 interactions, top by confidence:

A	B	Type	Score
CDR2	KTN1	psi-mi:“MI:0914”(association)	0.730
GOLGA6L2	SDHA	psi-mi:“MI:0915”(physical association)	0.400
GOLGA6L2	HSPA4	psi-mi:“MI:0915”(physical association)	0.400
GOLGA6L2	H2BC21	psi-mi:“MI:0915”(physical association)	0.400
GOLGA6L2	NUMA1	psi-mi:“MI:0915”(physical association)	0.400
GOLGA6L2	GOLGA6L6	psi-mi:“MI:0914”(association)	0.350
GOLGA6L2	CDR2	psi-mi:“MI:0915”(physical association)	0.000

ESM2 similar proteins: A0A0J9YX94, A0A0J9YXQ4, A0A0J9YY54, A0A494C1R9, A1L443, A5D7L8, A6NDY0, A6NKD2, E9PGG2, F6SZT2, O19110, O75807, O88852, P0CV98, P0CV99, P0CW00, P0CW01, P0CW24, P0DV79, P17564, P59644, P78358, Q01534, Q0P5N2, Q15735, Q2KI51, Q587J8, Q5R5G8, Q5R6R8, Q5RFC2, Q5SV97, Q60465, Q6P752, Q86V59, Q8BSI6, Q8N9W4, Q8NAG6, Q8NEE8, Q8VD63, Q95LS7

Diamond homologs: A0A1B0GV03, A1IH00, A6NC78, A6NCC3, A6NDK9, A6NDN3, A6NEF3, A6NEM1, A6NI86, A6NN73, A7E2F4, A8MQT2, A8MZA4, F8WBI6, H0YKK7, H0YM25, H3BPF8, H3BSY2, H3BV12, I6L899, P0CG33, P0CJ92, P0DX00, P0DX01, P0DX02, P0DX52, P0DX53, Q08379, Q62839, Q8N7Z2, Q8N9W4, Q921M4, Q9NYA3, A6NMD2, D6RF30, H3BQL2, Q0D2H9, Q9HBQ8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	11
Likely pathogenic	1
Uncertain significance	10
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (12)

Variant ID	HGVS	Classification
151222	GRCh38/hg38 15q11.2-13.1(chr15:23328044-28638603)x4	Pathogenic
394379	GRCh37/hg19 15q11.2-13.1(chr15:23300138-29338429)x3	Pathogenic
4846764	GRCh38/hg38 15q11.2(chr15:23223549-24426071)x1	Pathogenic
564142	GRCh37/hg19 15q11.2-13.1(chr15:22770421-28534245)x3	Pathogenic
564143	GRCh37/hg19 15q11.2-13.1(chr15:22770421-28545601)x4	Pathogenic
564144	GRCh37/hg19 15q11.2-13.1(chr15:22770421-28823722)x1	Pathogenic
564145	GRCh37/hg19 15q11.2-13.1(chr15:22770421-29069001)x1	Pathogenic
564162	GRCh37/hg19 15q11.2-12(chr15:23662481-25991024)x1	Pathogenic
625833	GRCh37/hg19 15q11.2-13.1(chr15:22816713-28530182)	Pathogenic
815689	GRCh37/hg19 15q11.2-12(chr15:23288374-27706996)x1	Pathogenic
997087	GRCh37/hg19 15q11.2-13.1(chr15:23208842-28525460)	Pathogenic
4279370	GRCh37/hg19 15q11.2(chr15:23615769-23816927)x1	Likely pathogenic

SpliceAI

1145 predictions. Top by Δscore:

Variant	Effect	Δscore
15:23441973:GCTCA:G	donor_loss	1.0000
15:23441974:CTCAC:C	donor_loss	1.0000
15:23441975:TCACC:T	donor_loss	1.0000
15:23441976:CACC:C	donor_loss	1.0000
15:23441977:A:C	donor_loss	1.0000
15:23441978:C:CG	donor_loss	1.0000
15:23442116:TTATG:T	acceptor_gain	1.0000
15:23442117:TATG:T	acceptor_gain	1.0000
15:23442118:ATG:A	acceptor_gain	1.0000
15:23442119:TG:T	acceptor_gain	1.0000
15:23442120:GC:G	acceptor_loss	1.0000
15:23442121:C:CC	acceptor_gain	1.0000
15:23442129:C:CT	acceptor_gain	1.0000
15:23442129:C:T	acceptor_gain	1.0000
15:23442130:G:T	acceptor_gain	1.0000
15:23442134:C:CT	acceptor_gain	1.0000
15:23442135:A:T	acceptor_gain	1.0000
15:23442136:G:C	acceptor_gain	1.0000
15:23442136:G:GC	acceptor_gain	1.0000
15:23442148:A:AC	acceptor_gain	1.0000
15:23442148:A:C	acceptor_gain	1.0000
15:23442448:A:AC	donor_gain	1.0000
15:23442449:C:CC	donor_gain	1.0000
15:23442454:T:A	donor_gain	1.0000
15:23442509:C:CC	acceptor_gain	1.0000
15:23443775:AC:A	donor_gain	1.0000
15:23443776:CC:C	donor_gain	1.0000
15:23443831:T:A	donor_gain	1.0000
15:23443989:T:A	donor_gain	1.0000
15:23444157:CTCA:C	donor_loss	1.0000

AlphaMissense

5899 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:23442103:A:G	L223P	0.962
15:23444048:A:G	L107P	0.961
15:23442019:A:G	L251P	0.954
15:23442462:A:G	L213P	0.948
15:23442082:A:G	L230P	0.934
15:23443837:A:C	F177L	0.933
15:23443837:A:T	F177L	0.933
15:23443839:A:G	F177L	0.933
15:23444027:A:G	L114P	0.929
15:23442070:A:G	L234P	0.928
15:23443856:A:G	L171S	0.923
15:23444039:T:G	Q110P	0.923
15:23442089:C:G	A228P	0.915
15:23441570:A:G	L302P	0.909
15:23444019:C:G	A117P	0.906
15:23441507:A:G	L323P	0.904
15:23447178:A:G	W2R	0.900
15:23447178:A:T	W2R	0.900
15:23444005:G:C	S121R	0.897
15:23444005:G:T	S121R	0.897
15:23444007:T:G	S121R	0.897
15:23441498:T:G	Q326P	0.894
15:23442478:C:G	A208P	0.887
15:23443826:A:G	L181S	0.885
15:23441486:A:G	L330P	0.880
15:23441567:C:G	R303P	0.878
15:23442007:A:G	L255P	0.878
15:23444172:C:G	R95P	0.878
15:23443951:G:C	F139L	0.875
15:23443951:G:T	F139L	0.875

dbSNP variants (sampled 300 via entrez): RS1000836889 (15:23446538 C>T), RS1001369281 (15:23446312 T>C), RS1002325232 (15:23442353 A>G), RS1002383915 (15:23447264 A>G), RS1002810998 (15:23448552 G>A,T), RS1002926813 (15:23443302 A>C), RS1003386992 (15:23448300 T>A), RS1003408050 (15:23443111 G>A), RS1004069016 (15:23442084 T>C,G), RS1005008817 (15:23448278 G>A,C,T), RS1005067854 (15:23443059 A>C,G), RS1005161211 (15:23443294 T>C), RS1005281177 (15:23448012 C>T), RS1007078856 (15:23445511 T>C), RS1007185094 (15:23445782 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:608636

GenCC curated gene-disease

Mondo (2): intellectual disability (MONDO:0001071), 15q11q13 microduplication syndrome (MONDO:0012081)

Orphanet (2): 15q11q13 microduplication syndrome (Orphanet:238446), NON RARE IN EUROPE: Unexplained intellectual disability (Orphanet:319658)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D008607	Intellectual Disability	C10.597.606.360; C23.888.592.604.646; F01.700.687; F03.625.539

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

2 total (human), top 2 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	increases expression	1
Silicon Dioxide	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05657860	PHASE4	COMPLETED	Guanfacine Extended Release for the Reduction of Aggression and Self-injurious Behavior Associated With Prader-Willi Syndrome
NCT05744479	PHASE4	RECRUITING	Metformin for Antipsychotic-induced Weight Gain in Adults With Intellectual Disability
NCT06107829	PHASE4	WITHDRAWN	Valbenazine Treatment of Tardive Dyskinesia in Adults With Intellectual/Developmental Disabilities
NCT06997198	PHASE4	NOT_YET_RECRUITING	Deutetrabenazine Treatment for Tardive Dyskinesia in Intellectual/Developmental Disabilities
NCT02270736	PHASE3	COMPLETED	Clinical Study to Investigate the Efficacy and Safety of NT 201 Compared to Placebo in the Treatment of Chronic Troublesome Drooling Associated With Neurological Disorders and/or Intellectual Disability
NCT02304302	PHASE2	COMPLETED	Down Syndrome Memantine Follow-up Study
NCT03862950	PHASE2	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome (Met)
NCT04529226	PHASE2	UNKNOWN	Study to Compare Clozapine vs Treatment as Usual in People With Intellectual Disability & Treatment-resistant Psychosis
NCT04821856	PHASE2	COMPLETED	Evaluation of the Effectiveness of Cannabidiol in Treating Severe Behavioural Problems in Children and Adolescents With Intellectual Disability
NCT05273320	PHASE1	COMPLETED	Clinical Trial of Nabilone for Aggression in Adults With Intellectual and Developmental Disabilities
NCT05301361	PHASE1	ENROLLING_BY_INVITATION	Sensitivity of the NIH Toolbox to Stimulant Treatment in Intellectual Disabilities
NCT06016764	PHASE1	COMPLETED	Use of MRI and cTBS for Catatonia in Autism
NCT06586827	PHASE1	COMPLETED	Impact of Competency-Based Training and Technical Assistance Employment Outcomes of Individuals With ID/DD
NCT07531940	PHASE1	NOT_YET_RECRUITING	Escalating Doses of Memantine in Down Syndrome (MEDS-123)
NCT03479476	PHASE2/PHASE3	COMPLETED	A Trial of Metformin in Individuals With Fragile X Syndrome
NCT02616796	PHASE1/PHASE2	COMPLETED	Effects of Social Gaze Training on Brain and Behavior in Fragile X Syndrome
NCT06860672	EARLY_PHASE1	RECRUITING	Clinical Trial of the Dual Vector Base Editor for the Treatment of the CHD3-R1025W Mutation
NCT00597948	Not specified	COMPLETED	Healthy Lifestyles for People With Intellectual Disabilities
NCT01087320	Not specified	RECRUITING	Genome Medical Sequencing for Gene Discovery
NCT01652963	Not specified	UNKNOWN	Picture-based Computerised Assessment and Training of Cognitive Behaviour Therapy Skills
NCT01695395	Not specified	COMPLETED	Mental Health Care Provision for Adults With Intellectual Disability and a Mental Disorder
NCT01867554	Not specified	COMPLETED	Research and Characterization of New Genes Involved in Intellectual Disability
NCT01915381	Not specified	COMPLETED	Improving Adherence Healthy Lifestyle With a Smartphone Application Based on Adults With Intellectual Disabilities
NCT01988623	Not specified	COMPLETED	Pivotal Response Treatment for Individuals With Intellectual Disabilities
NCT02099773	Not specified	COMPLETED	Support Staff-client Interactions With Augmentative and Alternative Communication
NCT02136849	Not specified	COMPLETED	Inter-regional Project of the Great Western Exploration Approach for Exome Molecular Causes Severe Intellectual Disability Isolated or Syndromic
NCT02225041	Not specified	COMPLETED	Sedation Strategy and Cognitive Outcome After Critical Illness in Early Childhood
NCT02414438	Not specified	COMPLETED	Establishing the Clinical Utility of First StepDx PLUS and NextStepDx PLUS Study
NCT02451761	Not specified	COMPLETED	Apparently Balanced Chromosomal Translocation/ Next-generation Sequencing/ Intellectual Disability
NCT02461420	Not specified	ACTIVE_NOT_RECRUITING	Mapping the Genotype, Phenotype, and Natural History of Phelan-McDermid Syndrome
NCT02461459	Not specified	ACTIVE_NOT_RECRUITING	Autism Spectrum Disorder (ASD) and Intellectual Disability (ID) Determinants in Tuberous Sclerosis Complex (TSC)
NCT02486081	Not specified	COMPLETED	Development and Application-Smart Football for Movement Evaluation and Training in the Special Education Population
NCT02504502	Not specified	COMPLETED	Enhancing Genomic Laboratory Reports to Enhance Communication and Empower Patients
NCT02513277	Not specified	COMPLETED	Diabetes Screening & Prevention for People With Learning (Intellectual) Disabilities:STOP Diabetes Study
NCT02561754	Not specified	COMPLETED	Weight Management for Adolescents With IDD
NCT02591446	Not specified	COMPLETED	Transcranial Magnetic Stimulation Studies in Autism Spectrum Disorders
NCT02714868	Not specified	COMPLETED	Evaluation of Project TEAM (Teens Making Environmental and Activity Modifications)
NCT02721394	Not specified	UNKNOWN	FCT With Young Children With ID in the UK: A Feasibility Project V.1
NCT02746614	Not specified	COMPLETED	Psychomotor Therapy Effects in Adaptive Behavior and Motor Proficiency in Intellectual Disability
NCT02836405	Not specified	COMPLETED	TMS for the Investigation of Brain Plasticity in Autism Spectrum Disorders