COL13A1

Summary

COL13A1 (collagen type XIII alpha 1 chain, HGNC:2190) is a protein-coding gene on chromosome 10q22.1, encoding Collagen alpha-1(XIII) chain (Q5TAT6). Involved in cell-matrix and cell-cell adhesion interactions that are required for normal development.

This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective tissues. Unlike most of the collagens, which are secreted into the extracellular matrix, collagen XIII contains a transmembrane domain and the protein has been localized to the plasma membrane. The transcripts for this gene undergo complex and extensive splicing involving at least eight exons. Like other collagens, collagen XIII is a trimer; it is not known whether this trimer is composed of one or more than one alpha chain isomer. A number of alternatively spliced transcript variants have been described, but the full length nature of some of them has not been determined.

Source: NCBI Gene 1305 — RefSeq curated summary.

At a glance

• Gene–disease (curated): congenital myasthenic syndrome 19 (Strong, GenCC) — +2 more curated relationships
• GWAS associations: 16
• Clinical variants (ClinVar): 852 total — 18 pathogenic, 26 likely-pathogenic
• Phenotypes (HPO): 113
• MANE Select transcript: NM_001368882

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:2190
Approved symbol	COL13A1
Name	collagen type XIII alpha 1 chain
Location	10q22.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000197467
Ensembl biotype	protein_coding
OMIM	120350
Entrez	1305

Gene structure

Transcript identifiers

Ensembl transcripts: 51 — 21 protein_coding_CDS_not_defined, 18 protein_coding, 8 nonsense_mediated_decay, 4 retained_intron

ENST00000354547, ENST00000357811, ENST00000398969, ENST00000398975, ENST00000398978, ENST00000456019, ENST00000478219, ENST00000479733, ENST00000484990, ENST00000517713, ENST00000518052, ENST00000520133, ENST00000520267, ENST00000522165, ENST00000645393, ENST00000673628, ENST00000673641, ENST00000673681, ENST00000673736, ENST00000673755, ENST00000673768, ENST00000673802, ENST00000673830, ENST00000673842, ENST00000673850, ENST00000673914, ENST00000673927, ENST00000673931, ENST00000673957, ENST00000673977, ENST00000674008, ENST00000674040, ENST00000674050, ENST00000674121, ENST00000674124, ENST00000682048, ENST00000682251, ENST00000682511, ENST00000682574, ENST00000682679, ENST00000682702, ENST00000682817, ENST00000683194, ENST00000683633, ENST00000683667, ENST00000683952, ENST00000683993, ENST00000684309, ENST00000684323, ENST00000684376, ENST00000684387

RefSeq mRNA: 16 — MANE Select: NM_001368882 NM_001130103, NM_001320951, NM_001368882, NM_001368883, NM_001368884, NM_001368885, NM_001368886, NM_001368895, NM_001368896, NM_001368897, NM_001368898, NM_080798, NM_080800, NM_080801, NM_080802, NM_080805

CCDS: CCDS44419, CCDS44423, CCDS44424, CCDS44425, CCDS44427, CCDS44428, CCDS91251, CCDS91252, CCDS91253, CCDS91254

Canonical transcript exons

ENST00000645393 — 41 exons

Exon	Start	End
ENSE00000933706	69904933	69904959
ENSE00000933712	69921882	69921935
ENSE00000933713	69922708	69922794
ENSE00000933714	69923802	69923855
ENSE00000933715	69924963	69925007
ENSE00000933716	69925804	69925872
ENSE00000933717	69928937	69928999
ENSE00000933718	69930043	69930087
ENSE00000933719	69930400	69930552
ENSE00001027060	69880503	69880553
ENSE00001027064	69872184	69872210
ENSE00001027075	69895550	69895576
ENSE00001273920	69889414	69889440
ENSE00001274043	69898697	69898762
ENSE00001274072	69917289	69917333
ENSE00001274079	69902748	69902855
ENSE00001274269	69887456	69887491
ENSE00001331090	69894675	69894701
ENSE00001331092	69894552	69894578
ENSE00001340904	69875128	69875163
ENSE00001340944	69888304	69888330
ENSE00001399563	69905787	69905822
ENSE00001403205	69940988	69941023
ENSE00001410950	69919062	69919088
ENSE00001424199	69918285	69918317
ENSE00001459923	69927087	69927110
ENSE00002506792	69867798	69867805
ENSE00003495675	69945671	69945724
ENSE00003497421	69936756	69936782
ENSE00003528817	69952882	69952968
ENSE00003533960	69944125	69944178
ENSE00003567527	69935350	69935391
ENSE00003582858	69878039	69878065
ENSE00003616834	69957004	69957042
ENSE00003635242	69947307	69947342
ENSE00003662732	69822369	69822438
ENSE00003680179	69937635	69937715
ENSE00003684302	69932560	69932604
ENSE00003816566	69958699	69959144
ENSE00003822221	69919665	69919727
ENSE00003896536	69801906	69802717

Expression profiles

Bgee: expression breadth ubiquitous, 209 present calls, max score 95.46.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.9759 / max 122.5539, expressed in 964 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
105359	3.6832	810
105360	1.7355	645
105358	0.2498	125
105364	0.0974	24
105363	0.0739	15
205889	0.0645	19
105362	0.0508	19
105361	0.0209	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
cerebellar hemisphere	UBERON:0002245	95.46	gold quality
cerebellar cortex	UBERON:0002129	95.38	gold quality
cerebellum	UBERON:0002037	94.92	gold quality
right hemisphere of cerebellum	UBERON:0014890	94.75	gold quality
blood vessel layer	UBERON:0004797	94.33	gold quality
periodontal ligament	UBERON:0008266	94.20	gold quality
tibia	UBERON:0000979	93.49	gold quality
corpus epididymis	UBERON:0004359	92.39	gold quality
ascending aorta	UBERON:0001496	89.54	gold quality
thoracic aorta	UBERON:0001515	89.40	gold quality
cauda epididymis	UBERON:0004360	89.32	gold quality
cerebellar vermis	UBERON:0004720	89.32	gold quality
aorta	UBERON:0000947	88.80	gold quality
popliteal artery	UBERON:0002250	88.41	gold quality
tibial artery	UBERON:0007610	88.37	gold quality
descending thoracic aorta	UBERON:0002345	88.22	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	87.97	gold quality
lower lobe of lung	UBERON:0008949	85.23	gold quality
lung	UBERON:0002048	83.74	gold quality
skin of hip	UBERON:0001554	82.64	gold quality
stromal cell of endometrium	CL:0002255	82.51	gold quality
trabecular bone tissue	UBERON:0002483	82.48	gold quality
upper lobe of left lung	UBERON:0008952	82.02	gold quality
upper lobe of lung	UBERON:0008948	81.87	gold quality
right lung	UBERON:0002167	81.77	gold quality
visceral pleura	UBERON:0002401	81.63	gold quality
triceps brachii	UBERON:0001509	81.57	gold quality
right coronary artery	UBERON:0001625	81.44	gold quality
right atrium auricular region	UBERON:0006631	79.89	gold quality
gluteal muscle	UBERON:0002000	79.51	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-7008	yes	68.96
E-CURD-112	yes	15.46
E-ANND-3	yes	5.73

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): FOXO1, FOXO3

Literature-anchored findings (GeneRIF, showing 15)

• The type XIII collagen ectodomain is a 150-nm rod and capable of binding to fibronectin, nidogen-2, perlecan, and heparin. (PMID:11956183)
• two widely separated coiled-coil domains of type XIII and related collagens function as independent oligomerization domains participating in the folding of distinct areas of the molecule. (PMID:12832406)
• Congenital myasthenic syndrome type 19 is caused by mutations in COL13A1. (PMID:26626625)
• We identified overexpression of collagen type XIII alpha 1 in active Thyroid-associated ophthalmopathy affected fat. (PMID:27245701)
• The combination of constitutively low expression of COL13A1, high physiological and metabolic demands, and consequentially relatively high exposure to stressors may explain the particular vulnerability of inferior rectus to thyroid-associated ophthalmopathy. (PMID:27580012)
• this study shows that COL13A1 production by urothelial carcinoma of the bladder plays a pivotal role in tumor invasion through the induction of tumor budding (PMID:28415608)
• Urine levels of COL4A1, COL13A1, the combined values of COL4A1 and COL13A1 (COL4A1 + COL13A1), and CYFRA21-1 were significantly elevated in urine from patients with BCa compared to the controls. A high urinary COL4A1 + COL13A1 was found to be an independent risk factor for intravesical recurrence. (PMID:28837258)
• Findings suggest a significant association between variants in COL13A1, ADIPOQ, SAMM50, and PNPLA3, and risk of NAFLD/elevated transaminase levels in Mexican adults with an admixed ancestry. (PMID:29307798)
• The authors report a congenital myasthenic syndrome due to mutations in COL13A1, which encodes an extracellular matrix protein that is concentrated at the neuromuscular junction and highlights a role for these extracellular matrix proteins in maintaining synaptic stability that is independent of the AGRN/MuSK clustering pathway. (PMID:29363764)
• It was established that the frequency of individuals with the COL13A1*D/*D genotype was higher in the senile age period. The LAMA2*I/*D genotype was predisposing to longevity among women. (PMID:29369589)
• Results indicate a function of collagen XIII in promoting cancer metastasis, cell invasion, and anoikis resistance. (PMID:30285809)
• The data of this study support the causality of COL13A1 variants for Congenital myasthenic syndrome. (PMID:30767057)
• patients with COL13A1 mutations present mostly with severe early-onset myasthenic syndrome with feeding and breathing difficulties (PMID:31081514)
• Data suggest that ColXIII has a role in age-dependent cortical bone deterioration with possible implications for osteoporosis and fracture risk. (PMID:31220558)
• TGF-beta2 and collagen play pivotal roles in the spheroid formation and anti-aging of human dermal papilla cells. (PMID:34404755)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
mus_musculus	Col13a1	ENSMUSG00000058806
rattus_norvegicus	Col13a1	ENSRNOG00000000552
caenorhabditis_elegans		WBGENE00000674

Paralogs (37): COL9A2 (ENSG00000049089), COL23A1 (ENSG00000050767), COL11A1 (ENSG00000060718), COL17A1 (ENSG00000065618), COL5A3 (ENSG00000080573), COL4A4 (ENSG00000081052), COL16A1 (ENSG00000084636), COL9A3 (ENSG00000092758), COL20A1 (ENSG00000101203), COL1A1 (ENSG00000108821), COL9A1 (ENSG00000112280), COL7A1 (ENSG00000114270), COL21A1 (ENSG00000124749), COL5A1 (ENSG00000130635), COL4A2 (ENSG00000134871), COL2A1 (ENSG00000139219), COL6A1 (ENSG00000142156), COL6A2 (ENSG00000142173), EDA (ENSG00000158813), COL26A1 (ENSG00000160963), COL1A2 (ENSG00000164692), COL3A1 (ENSG00000168542), COL4A3 (ENSG00000169031), COL22A1 (ENSG00000169436), COL24A1 (ENSG00000171502), COL18A1 (ENSG00000182871), EMID1 (ENSG00000186998), COL4A1 (ENSG00000187498), COL4A5 (ENSG00000188153), COL25A1 (ENSG00000188517), COL27A1 (ENSG00000196739), COL4A6 (ENSG00000197565), COL11A2 (ENSG00000204248), COL5A2 (ENSG00000204262), COL15A1 (ENSG00000204291), COLQ (ENSG00000206561), COL28A1 (ENSG00000215018)

Protein

Protein identifiers

Collagen alpha-1(XIII) chain — Q5TAT6 (reviewed: Q5TAT6)

Alternative names: COLXIIIA1

All UniProt accessions (19): A0A2R8YGI3, A0A669KA03, A0A669KAZ4, A0A669KB16, A0A669KB25, A0A669KB28, A0A669KB39, A0A669KB54, A0A669KB55, A0A669KB79, A0A669KBB8, A0A669KBE0, A0A669KBF9, A0A6E1W314, Q5TAT6, E7ES50, E7EX21, H7BYT9, H7BZB6

UniProt curated annotations — full annotation on UniProt →

Function. Involved in cell-matrix and cell-cell adhesion interactions that are required for normal development. May participate in the linkage between muscle fiber and basement membrane. May play a role in endochondral ossification of bone and branching morphogenesis of lung. Binds heparin. At neuromuscular junctions, may play a role in acetylcholine receptor clustering.

Subunit / interactions. Homotrimer; disulfide-linked. Nucleation of the type XIII collagen triple helix is likely to occur at the N-terminal region with triple helix formation proceeding from the N- to the C-terminus. Interacts with FN1, perlecan/HSPG2 and NID2.

Subcellular location. Cell membrane. Postsynaptic cell membrane.

Tissue specificity. Widely expressed in both fetal and adult ocular tissues (at protein level). In the eye, expression is accentuated in the ciliary muscle, optic nerve and the neural retina. In early placenta, localized to fibroblastoid stromal cells of the placental villi, to endothelial cells of developing capillaries and to cells of the cytotrophoblastic columns. Also detected in large decidual cells of the decidual membrane and to stromal cells of the gestational endometrium, but not in the epithelial cells in the endometrial glands. Isoform 10: Expressed in muscle.

Disease relevance. Myasthenic syndrome, congenital, 19 (CMS19) [MIM:616720] A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness affecting the axial and limb muscles (with hypotonia in early-onset forms), the ocular muscles (leading to ptosis and ophthalmoplegia), and the facial and bulbar musculature (affecting sucking and swallowing, and leading to dysphonia). The symptoms fluctuate and worsen with physical effort. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (11)

UniProt ID	Names	Canonical?
Q5TAT6-1	1	yes
Q5TAT6-2	2
Q5TAT6-3	3
Q5TAT6-4	4
Q5TAT6-5	5
Q5TAT6-6	6
Q5TAT6-7	7
Q5TAT6-8	8
Q5TAT6-9	9
Q5TAT6-10	10
Q5TAT6-11	11

RefSeq proteins (16): NP_001123575, NP_001307880, NP_001355811, NP_001355812, NP_001355813, NP_001355814, NP_001355815, NP_001355824, NP_001355825, NP_001355826, NP_001355827, NP_542988, NP_542990, NP_542991, NP_542992, NP_542995 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR008160	Collagen	Repeat
IPR050938	Collagen_Structural_Proteins	Family

Pfam: PF01391

UniProt features (57 total): compositionally biased region 16, sequence conflict 16, region of interest 11, splice variant 9, topological domain 2, chain 1, transmembrane region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5TAT6-F1	55.67	0.02

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-1442490	Collagen degradation
R-HSA-1650814	Collagen biosynthesis and modifying enzymes
R-HSA-216083	Integrin cell surface interactions
R-HSA-8948216	Collagen chain trimerization

MSigDB gene sets: 416 (showing top): HNF3ALPHA_Q6, GOBP_SKELETAL_SYSTEM_DEVELOPMENT, GOCC_COLLAGEN_TRIMER, LI_WILMS_TUMOR, MEF2_02, GGGTGGRR_PAX4_03, CHANDRAN_METASTASIS_DN, FOXD3_01, GOBP_REPLACEMENT_OSSIFICATION, GOBP_CELL_CELL_ADHESION, CEBP_Q2, GOBP_ANIMAL_ORGAN_MORPHOGENESIS, GOBP_BONE_DEVELOPMENT, GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT, LI_WILMS_TUMOR_VS_FETAL_KIDNEY_1_DN

GO Biological Process (7): morphogenesis of a branching structure (GO:0001763), endochondral ossification (GO:0001958), cell-matrix adhesion (GO:0007160), cell differentiation (GO:0030154), cell-cell adhesion (GO:0098609), ossification (GO:0001503), cell adhesion (GO:0007155)

GO Molecular Function (3): heparin binding (GO:0008201), extracellular matrix structural constituent conferring tensile strength (GO:0030020), protein binding (GO:0005515)

GO Cellular Component (11): extracellular region (GO:0005576), collagen type XIII trimer (GO:0005600), basement membrane (GO:0005604), endoplasmic reticulum lumen (GO:0005788), plasma membrane (GO:0005886), extracellular matrix (GO:0031012), postsynaptic membrane (GO:0045211), collagen trimer (GO:0005581), cell-cell junction (GO:0005911), membrane (GO:0016020), synapse (GO:0045202)

Reactome top-level categories

Rollup of top-4 pathways:

Category	Pathways
Degradation of the extracellular matrix	1
Collagen formation	1
Extracellular matrix organization	1
Collagen biosynthesis and modifying enzymes	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
multicellular organismal process	2
cellular anatomical structure	2
anatomical structure morphogenesis	1
replacement ossification	1
endochondral bone morphogenesis	1
cell-substrate adhesion	1
cellular developmental process	1
cell adhesion	1
cellular process	1
glycosaminoglycan binding	1
sulfur compound binding	1
extracellular matrix structural constituent	1
binding	1
transmembrane collagen trimer	1
extracellular matrix	1
endoplasmic reticulum	1
intracellular organelle lumen	1
membrane	1
cell periphery	1
external encapsulating structure	1
synaptic membrane	1
postsynapse	1
protein-containing complex	1
anchoring junction	1
cell junction	1

Protein interactions and networks

STRING

1286 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
COL13A1	P4HA1	P13674	658
COL13A1	HSPG2	P98160	508
COL13A1	COLQ	Q9Y215	495
COL13A1	CDH17	Q12864	488
COL13A1	COL4A2	P08572	461
COL13A1	COL27A1	Q8IZC6	446
COL13A1	COL16A1	Q07092	442
COL13A1	COL5A3	P25940	440
COL13A1	COL5A1	P20908	440
COL13A1	COL4A3	Q01955	428
COL13A1	COL4A1	P02462	427
COL13A1	COL12A1	Q99715	411
COL13A1	HIGD1B	Q9P298	407
COL13A1	KCNS1	Q96KK3	403
COL13A1	ATOH7	Q8N100	394

IntAct

11 interactions, top by confidence:

A	B	Type	Score
MMP2	COL4A1	psi-mi:“MI:0914”(association)	0.640
PLOD3	PLOD2	psi-mi:“MI:0914”(association)	0.530
LAIR2	LAMA5	psi-mi:“MI:0914”(association)	0.530
COL13A1	HMGA1	psi-mi:“MI:0915”(physical association)	0.400
LAIR2	PLOD3	psi-mi:“MI:0914”(association)	0.350
LAIR2	AGRN	psi-mi:“MI:0914”(association)	0.350
PLOD1	PLOD2	psi-mi:“MI:0914”(association)	0.350
COLGALT2	PLOD2	psi-mi:“MI:0914”(association)	0.350
SYNPR	SPAG9	psi-mi:“MI:0914”(association)	0.350

BioGRID (11): COL13A1 (Proximity Label-MS), COL13A1 (Protein-RNA), COL13A1 (Proximity Label-MS), COL13A1 (Affinity Capture-MS), COL13A1 (Affinity Capture-MS), COL13A1 (Affinity Capture-MS), COL13A1 (Affinity Capture-MS), COL13A1 (Affinity Capture-MS), COL13A1 (Affinity Capture-MS), COL13A1 (Affinity Capture-MS), HIST1H4A (Cross-Linking-MS (XL-MS))

ESM2 similar proteins: C0HLH0, C0HLH4, C0HLI6, C0HLN2, P02460, P02462, P02463, P05997, P08120, P08122, P08125, P08572, P12106, P12107, P12108, P13942, P20849, P20850, P20909, P23206, P25318, P27393, P29400, P30754, P32017, P70560, Q01955, Q03692, Q05306, Q05722, Q07643, Q0VF58, Q14031, Q14050, Q14055, Q14993, Q28083, Q28247, Q32S24, Q3U962

Diamond homologs: Q5TAT6, Q9R1N9, Q86Y22

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 12 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
Collagen biosynthesis and modifying enzymes	5	77.5×	2e-07

GO biological processes:

GO term	Partners	Fold	FDR
collagen fibril organization	5	102.1×	4e-08

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	18
Likely pathogenic	26
Uncertain significance	266
Likely benign	374
Benign	117

Top pathogenic / likely-pathogenic (30)

Variant ID	HGVS	Classification
1184983	NM_001368882.1(COL13A1):c.1884_1886delinsCCCT (p.Ser629fs)	Pathogenic
1184984	NM_001368882.1(COL13A1):c.675C>G (p.Tyr225Ter)	Pathogenic
1184985	NM_001368882.1(COL13A1):c.1619del (p.Asn540fs)	Pathogenic
1444676	NM_001368882.1(COL13A1):c.55_62del (p.Glu19fs)	Pathogenic
1455951	NM_001368882.1(COL13A1):c.330_354del (p.Pro111fs)	Pathogenic
218905	NM_001368882.1(COL13A1):c.1206del (p.Leu403fs)	Pathogenic
218906	NC_000010.11:g.69888305del	Pathogenic
2748230	NM_001368882.1(COL13A1):c.685-1210_685-1204del	Pathogenic
280688	NM_001368882.1(COL13A1):c.271C>T (p.Arg91Ter)	Pathogenic
280690	NM_001368882.1(COL13A1):c.648del (p.Gly217fs)	Pathogenic
2821165	NM_001368882.1(COL13A1):c.2062G>T (p.Glu688Ter)	Pathogenic
2895874	NM_001368882.1(COL13A1):c.76del (p.Val26fs)	Pathogenic
3689777	NM_001368882.1(COL13A1):c.1288G>T (p.Glu430Ter)	Pathogenic
423752	NM_001368882.1(COL13A1):c.1503dup (p.Gly502fs)	Pathogenic
4715602	NM_001368882.1(COL13A1):c.362dup (p.Gly122fs)	Pathogenic
4720513	NM_001368882.1(COL13A1):c.1220_1221insT (p.Gly408fs)	Pathogenic
975954	NM_001368882.1(COL13A1):c.1138C>T (p.Gln380Ter)	Pathogenic
982128	NM_001368882.1(COL13A1):c.1559G>A (p.Gly520Asp)	Pathogenic
1066217	NM_001368882.1(COL13A1):c.1284+1G>A	Likely pathogenic
1066742	NM_001368882.1(COL13A1):c.1285-1G>C	Likely pathogenic
1189395	NM_001368882.1(COL13A1):c.435+2T>G	Likely pathogenic
1322106	NM_001368882.1(COL13A1):c.1230+1G>A	Likely pathogenic
1476402	NM_001368882.1(COL13A1):c.1230+1G>C	Likely pathogenic
1482812	NM_001368882.1(COL13A1):c.550-2A>G	Likely pathogenic
1504717	NM_001368882.1(COL13A1):c.967-2A>G	Likely pathogenic
1690748	NM_001368882.1(COL13A1):c.462+2T>C	Likely pathogenic
1698998	NM_001368882.1(COL13A1):c.1026+1G>A	Likely pathogenic
1959257	NM_001368882.1(COL13A1):c.1231-1G>A	Likely pathogenic
2007345	NM_001368882.1(COL13A1):c.513+1G>T	Likely pathogenic
2412708	NM_001368882.1(COL13A1):c.803del (p.Pro268fs)	Likely pathogenic

SpliceAI

6224 predictions. Top by Δscore:

Variant	Effect	Δscore
10:69887492:G:GA	donor_loss	1.0000
10:69887492:G:GG	donor_gain	1.0000
10:69887493:TAAGT:T	donor_loss	1.0000
10:69904922:T:A	acceptor_gain	1.0000
10:69904928:CACAG:C	acceptor_loss	1.0000
10:69904930:CAGGG:C	acceptor_loss	1.0000
10:69904931:AGGGC:A	acceptor_loss	1.0000
10:69905821:AGG:A	donor_loss	1.0000
10:69905823:G:GA	donor_loss	1.0000
10:69905824:T:G	donor_loss	1.0000
10:69928539:C:G	donor_gain	1.0000
10:69937632:CAG:C	acceptor_loss	1.0000
10:69937633:A:AG	acceptor_gain	1.0000
10:69937633:AG:A	acceptor_gain	1.0000
10:69937633:AGG:A	acceptor_gain	1.0000
10:69937633:AGGG:A	acceptor_gain	1.0000
10:69937633:AGGGG:A	acceptor_gain	1.0000
10:69937634:G:GG	acceptor_gain	1.0000
10:69937634:G:GT	acceptor_loss	1.0000
10:69937634:GG:G	acceptor_gain	1.0000
10:69937634:GGG:G	acceptor_gain	1.0000
10:69937634:GGGG:G	acceptor_gain	1.0000
10:69937634:GGGGG:G	acceptor_gain	1.0000
10:69937714:CCG:C	donor_loss	1.0000
10:69937715:CG:C	donor_loss	1.0000
10:69937716:G:GG	donor_gain	1.0000
10:69937717:T:TG	donor_loss	1.0000
10:69937718:AA:A	donor_loss	1.0000
10:69944123:AG:A	acceptor_gain	1.0000
10:69944124:GG:G	acceptor_gain	1.0000

AlphaMissense

4538 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
10:69952960:T:C	C702R	0.998
10:69952961:G:A	C702Y	0.997
10:69952962:C:G	C702W	0.997
10:69957031:T:C	C714R	0.997
10:69952960:T:A	C702S	0.996
10:69952961:G:C	C702S	0.996
10:69957031:T:A	C714S	0.996
10:69957032:G:C	C714S	0.996
10:69957032:G:A	C714Y	0.993
10:69937708:G:A	G613E	0.992
10:69940989:G:A	G616E	0.992
10:69957033:C:G	C714W	0.992
10:69930062:G:A	G491D	0.991
10:69944135:G:A	G631E	0.991
10:69944153:G:A	G637D	0.991
10:69952910:G:A	G685E	0.991
10:69957036:G:C	W715C	0.991
10:69957036:G:T	W715C	0.991
10:69944126:G:A	G628D	0.990
10:69947317:G:A	G667E	0.990
10:69952900:G:C	G682R	0.990
10:69930053:G:A	G488E	0.989
10:69940998:G:A	G619D	0.989
10:69941007:G:A	G622D	0.989
10:69952918:G:T	G688W	0.989
10:69952961:G:T	C702F	0.989
10:69880537:G:A	G157D	0.988
10:69937699:G:A	G610D	0.988
10:69941016:G:A	G625E	0.988
10:69944144:G:A	G634E	0.988

dbSNP variants (sampled 300 via entrez): RS1000010846 (10:69883524 C>G,T), RS1000012450 (10:69848572 C>T), RS1000019432 (10:69850632 C>A,T), RS1000027993 (10:69848552 C>T), RS1000028813 (10:69948283 T>C), RS1000040448 (10:69854944 C>T), RS1000081256 (10:69954694 G>A), RS1000085651 (10:69848363 C>T), RS1000089930 (10:69916896 G>C), RS1000097353 (10:69805515 A>G), RS1000097413 (10:69883987 T>TA), RS1000131373 (10:69842385 C>T), RS1000134322 (10:69900994 C>T), RS1000162682 (10:69829017 T>C), RS1000214403 (10:69829201 T>C)

Disease associations

OMIM: gene MIM:120350 | disease phenotypes: MIM:616720, MIM:615935

GenCC curated gene-disease

Disease	Classification	Inheritance
congenital myasthenic syndrome 19	Strong	Autosomal recessive
postsynaptic congenital myasthenic syndrome	Supportive	Autosomal recessive
presynaptic congenital myasthenic syndrome	Supportive	Autosomal dominant

Mondo (4): congenital myasthenic syndrome 19 (MONDO:0014745), pancreatic agenesis 2 (MONDO:0014406), postsynaptic congenital myasthenic syndrome (MONDO:0020344), (MONDO:0020345)

Orphanet (2): Congenital myasthenic syndrome (Orphanet:590), Partial pancreatic agenesis (Orphanet:2805)

HPO phenotypes

113 total (30 of 113 shown, HPO-id order):

HPO	Term
HP:0000007	Autosomal recessive inheritance
HP:0000218	High palate
HP:0000276	Long face
HP:0000278	Retrognathia
HP:0000308	Microretrognathia
HP:0000347	Micrognathia
HP:0000369	Low-set ears
HP:0000407	Sensorineural hearing impairment
HP:0000467	Neck muscle weakness
HP:0000496	Abnormality of eye movement
HP:0000508	Ptosis
HP:0000565	Esotropia
HP:0000597	Ophthalmoparesis
HP:0000602	Ophthalmoplegia
HP:0000639	Nystagmus
HP:0000651	Diplopia
HP:0000768	Pectus carinatum
HP:0000961	Cyanosis
HP:0001249	Intellectual disability
HP:0001250	Seizure
HP:0001251	Ataxia
HP:0001252	Hypotonia
HP:0001265	Hyporeflexia
HP:0001270	Motor delay
HP:0001283	Bulbar palsy
HP:0001284	Areflexia
HP:0001288	Gait disturbance
HP:0001290	Generalized hypotonia
HP:0001315	Reduced tendon reflexes
HP:0001324	Muscle weakness

GWAS associations

16 associations (top):

Study	Trait	p-value
GCST000766_13	Non-alcoholic fatty liver disease histology (lobular)	7.000000e-06
GCST000766_2	Non-alcoholic fatty liver disease histology (lobular)	2.000000e-07
GCST002077_3	Parkinson’s disease	6.000000e-07
GCST002548_2	Ulcerative colitis	5.000000e-06
GCST002984_1	Early childhood aggressive behavior	2.000000e-06
GCST002985_4	Middle childhood and early adolescence aggressive behavior	3.000000e-06
GCST003487_4	Response to fenofibrate (total cholesterol levels)	2.000000e-06
GCST005331_6	CSF tryptophan concentration in tuberculous meningitis	7.000000e-06
GCST005351_2	Carboplatin disposition in epthelial ovarian cancer	4.000000e-06
GCST006107_16	Upper eyelid morphology	4.000000e-06
GCST007356_1	Antidepressant treatment resistance (number of drugs prescribed)	2.000000e-07
GCST009028_53	Adverse response to drug	7.000000e-07
GCST009462_105	Optic disc size	3.000000e-09
GCST010320_88	PR interval	1.000000e-09
GCST010321_38	PR interval	4.000000e-09
GCST011742_30	Triglyceride levels in HIV infection	2.000000e-06

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0007806	total cholesterol change measurement
EFO:0008534	tryptophan measurement
EFO:0009658	adverse effect
EFO:0004462	PR interval
EFO:0004530	triglyceride measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

61 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases expression, decreases methylation	6
Benzo(a)pyrene	affects methylation, decreases expression, affects expression	4
trichostatin A	affects cotreatment, increases expression	3
bisphenol A	affects cotreatment, decreases methylation, decreases expression	2
sodium arsenite	decreases expression, increases expression	2
entinostat	increases expression, affects cotreatment	2
Calcitriol	increases expression	2
Cisplatin	affects expression, decreases expression	2
Estradiol	decreases expression, increases expression, affects cotreatment	2
Oxygen	decreases expression, increases expression, increases reaction	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tetrachlorodibenzodioxin	affects expression, increases expression	2
Tretinoin	decreases expression, increases expression	2
sotorasib	decreases expression, affects cotreatment	1
methylmercuric chloride	decreases expression	1
propionaldehyde	increases expression	1
titanium dioxide	affects binding, decreases expression	1
mono-(2-ethylhexyl)phthalate	increases expression	1
cobaltous chloride	affects binding, increases reaction	1
butyraldehyde	increases expression	1
benzo(e)pyrene	affects methylation	1
aflatoxin B2	increases methylation	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression, affects response to substance, increases expression	1
pentanal	increases expression	1
seocalcitol	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression, decreases expression	1
dimethylarsinous acid	decreases expression	1
ormosil	affects binding, increases expression	1
dorsomorphin	affects cotreatment, increases expression, decreases expression	1
trametinib	decreases expression, affects cotreatment	1

Clinical trials (associated diseases)

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