DMRTC1

Summary

DMRTC1 (DMRT like family C1, HGNC:13910) is a protein-coding gene on chromosome Xq13.1, encoding Doublesex- and mab-3-related transcription factor C1 (Q5HYR2).

Predicted to be involved in regulation of DNA-templated transcription. Predicted to be located in chromatin. Predicted to be active in nucleus.

Source: NCBI Gene 63947 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 17 total — 2 pathogenic
• MANE Select transcript: NM_033053

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:13910
Approved symbol	DMRTC1
Name	DMRT like family C1
Location	Xq13.1
Locus type	gene with protein product
Status	Approved
Aliases	DMRT8
Ensembl gene	ENSG00000269502
Ensembl biotype	protein_coding
OMIM	300878
Entrez	63947

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 nonsense_mediated_decay

ENST00000595412, ENST00000596389, ENST00000615063, ENST00000622727

RefSeq mRNA: 3 — MANE Select: NM_033053 NM_001386923, NM_001386924, NM_033053

CCDS: CCDS35333

Canonical transcript exons

ENST00000615063 — 7 exons

Exon	Start	End
ENSE00002999492	72874825	72874958
ENSE00003006227	72875631	72875788
ENSE00003048539	72873550	72873697
ENSE00003158968	72873882	72873942
ENSE00003211374	72875273	72875331
ENSE00003711775	72943575	72943837
ENSE00003920605	72872025	72872564

Expression profiles

Bgee: expression breadth ubiquitous, 114 present calls, max score 71.72.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adenohypophysis	UBERON:0002196	71.72	gold quality
pituitary gland	UBERON:0000007	71.66	gold quality
right hemisphere of cerebellum	UBERON:0014890	70.47	gold quality
cerebellar hemisphere	UBERON:0002245	70.05	gold quality
cerebellum	UBERON:0002037	69.59	gold quality
cerebellar cortex	UBERON:0002129	69.53	gold quality
superior frontal gyrus	UBERON:0002661	69.12	gold quality
nucleus accumbens	UBERON:0001882	68.15	gold quality
anterior cingulate cortex	UBERON:0009835	66.66	gold quality
right frontal lobe	UBERON:0002810	65.96	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	65.04	gold quality
hypothalamus	UBERON:0001898	64.32	gold quality
Brodmann (1909) area 9	UBERON:0013540	64.18	gold quality
caudate nucleus	UBERON:0001873	64.01	gold quality
brain	UBERON:0000955	63.79	gold quality
cerebral cortex	UBERON:0000956	62.07	gold quality
putamen	UBERON:0001874	61.77	gold quality
ganglionic eminence	UBERON:0004023	61.66	gold quality
bone marrow cell	CL:0002092	61.47	gold quality
left ovary	UBERON:0002119	61.38	gold quality
left lobe of thyroid gland	UBERON:0001120	60.72	gold quality
frontal cortex	UBERON:0001870	60.72	gold quality
right ovary	UBERON:0002118	60.44	gold quality
ovary	UBERON:0000992	59.76	gold quality
thyroid gland	UBERON:0002046	59.74	gold quality
temporal lobe	UBERON:0001871	59.33	gold quality
Ammon’s horn	UBERON:0001954	59.25	gold quality
right lobe of thyroid gland	UBERON:0001119	58.98	gold quality
amygdala	UBERON:0001876	58.95	gold quality
body of pancreas	UBERON:0001150	57.90	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.62

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting DMRTC1, 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-4795-3P	100.00	74.62	4024
HSA-MIR-196A-1-3P	99.99	72.15	2772
HSA-MIR-513B-5P	99.99	69.96	2150
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-4524A-3P	99.72	66.85	2406
HSA-MIR-4499	99.62	67.29	1470
HSA-MIR-4643	99.49	67.63	1791
HSA-MIR-6722-3P	99.45	67.62	1919
HSA-MIR-1909-3P	99.03	66.56	1662
HSA-MIR-6761-5P	98.71	68.03	1504
HSA-MIR-7850-5P	98.12	67.28	1111
HSA-MIR-4421	97.99	64.89	701
HSA-MIR-4257	97.86	68.05	1190
HSA-MIR-5699-3P	97.81	65.00	861
HSA-MIR-4799-3P	97.78	65.97	893
HSA-MIR-3189-5P	97.55	66.71	655
HSA-MIR-4720-5P	97.46	65.67	893
HSA-MIR-5588-5P	97.46	65.70	913
HSA-MIR-4475	97.36	66.95	761
HSA-MIR-1243	97.07	65.44	719
HSA-MIR-3622A-3P	97.06	66.43	1000
HSA-MIR-3622B-3P	96.82	66.36	988

Cross-species orthologs

5 orthologs

Organism	Symbol	Gene ID
drosophila_melanogaster	dmrt99B	FBGN0039683
caenorhabditis_elegans		WBGENE00007776
caenorhabditis_elegans		WBGENE00017326
caenorhabditis_elegans		WBGENE00019521
caenorhabditis_elegans		WBGENE00022060

Paralogs (8): DMRT3 (ENSG00000064218), DMRT1 (ENSG00000137090), DMRTC2 (ENSG00000142025), DMRTA2 (ENSG00000142700), DMRTB1 (ENSG00000143006), DMRT2 (ENSG00000173253), DMRTA1 (ENSG00000176399), DMRTC1B (ENSG00000184911)

Protein

Protein identifiers

Doublesex- and mab-3-related transcription factor C1 — Q5HYR2 (reviewed: Q5HYR2)

All UniProt accessions (3): Q5HYR2, A0A087X258, G3V190

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Predominantly expressed in kidney, pancreas, ovary and testis. Detected in brain and in many other tissues.

Similarity. Belongs to the DMRT family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q5HYR2-1	1	yes
Q5HYR2-2	2

RefSeq proteins (3): NP_001373852, NP_001373853, NP_149042* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026607	DMRT	Family
IPR031577	DMRT-C1/C2_C	Domain

Pfam: PF15791

UniProt features (3 total): chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q5HYR2-F1	63.45	0.09

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 21 (showing top): SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, ACEVEDO_METHYLATED_IN_LIVER_CANCER_DN, GOMF_SEQUENCE_SPECIFIC_DNA_BINDING, MIKKELSEN_ES_HCP_WITH_H3_UNMETHYLATED, MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED, chrXq13, BAKKER_FOXO3_TARGETS_DN, GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY, MIR196A_1_3P, MIR507, MIR4524A_3P, MIR557, MIR5699_3P, MIR4475, MIR3189_5P

GO Biological Process (1): regulation of DNA-templated transcription (GO:0006355)

GO Molecular Function (0):

GO Cellular Component (2): chromatin (GO:0000785), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
DNA-templated transcription	1
regulation of gene expression	1
regulation of RNA biosynthetic process	1
chromosome	1
cellular anatomical structure	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

250 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
DMRTC1	UBN2	Q6ZU65	427
DMRTC1	CHIC1	Q5VXU3	396
DMRTC1	TTLL4	Q14679	389
DMRTC1	CTPS2	Q9NRF8	336
DMRTC1	RLIM	Q9NVW2	325
DMRTC1	RFX2	P48378	321
DMRTC1	SEL1L2	Q5TEA6	308
DMRTC1	HS6ST2	Q96MM7	300
DMRTC1	CDX4	O14627	296
DMRTC1	DMRT1	Q9Y5R6	279
DMRTC1	IL1RAPL1	Q9NZN1	270
DMRTC1	SLC7A2	P52569	262
DMRTC1	EFCAB5	A4FU69	245
DMRTC1	TMEM125	Q96AQ2	245
DMRTC1	WSCD1	Q658N2	244

IntAct

3 interactions, top by confidence:

A	B	Type	Score
DMRTC1	SIN3A	psi-mi:“MI:0915”(physical association)	0.370
DMRTC1	PTPN11	psi-mi:“MI:0915”(physical association)	0.370

BioGRID (3): DMRTC1 (Two-hybrid), DMRTC1B (Two-hybrid), DMRTC1 (Affinity Capture-MS)

ESM2 similar proteins: A0A096LP49, A0A1B0GVZ6, A0A1W2PR82, A5PL33, A6NDZ8, A6NE82, A6NJB7, A6QP24, A8MYA2, A8MZG2, B2RW88, D4AAA5, H7C350, O43593, O60393, O75593, O88621, P0C1T1, P59942, Q0P5M0, Q2KIS6, Q32LE6, Q3UN58, Q3ZCQ2, Q5BMD4, Q5HYR2, Q5JPB2, Q5M844, Q5SZB4, Q5VZ46, Q6GQX2, Q6NS69, Q6PAC4, Q80TS7, Q8BT88, Q8CGW9, Q8IWN7, Q8IXT2, Q8IYS4, Q8N1L9

Diamond homologs: A2A9A2, A2A9I7, A4QNP7, A6QQ94, A8TSS9, B0I1G7, B7ZS42, C0LZJ1, D4A218, F6W2R2, G5EEJ1, J7FCF0, O18214, P23023, P57690, P83758, P85119, Q18248, Q19291, Q2I327, Q2MJB4, Q32LE6, Q3LH63, Q4AE28, Q4QR87, Q5HYR2, Q5UU75, Q5VZB9, Q6YHU8, Q71MM5, Q76L87, Q801F8, Q80WT2, Q8BG36, Q8CFG4, Q8CGW9, Q8IXT2, Q8JIR6, Q90WM5, Q96MA1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	15
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
209109	NC_000023.10:g.71681853_72434328del752476	Pathogenic
559586	Single allele	Pathogenic

SpliceAI

749 predictions. Top by Δscore:

Variant	Effect	Δscore
X:72873873:T:A	donor_gain	1.0000
X:72875327:CCCAG:C	acceptor_gain	1.0000
X:72875328:CCAGC:C	acceptor_gain	1.0000
X:72875329:CAG:C	acceptor_gain	1.0000
X:72875332:C:CC	acceptor_gain	1.0000
X:72875629:A:AC	donor_gain	1.0000
X:72875630:C:CA	donor_gain	1.0000
X:72875698:C:CA	donor_gain	1.0000
X:72872563:AGC:A	acceptor_loss	0.9900
X:72872564:GC:G	acceptor_loss	0.9900
X:72872566:T:G	acceptor_loss	0.9900
X:72873699:T:C	acceptor_loss	0.9900
X:72875266:T:A	donor_gain	0.9900
X:72875267:CCTTA:C	donor_loss	0.9900
X:72875268:CTTA:C	donor_loss	0.9900
X:72875269:TTA:T	donor_loss	0.9900
X:72875270:TA:T	donor_loss	0.9900
X:72875271:ACCT:A	donor_gain	0.9900
X:72875272:CCTC:C	donor_gain	0.9900
X:72875274:T:TA	donor_gain	0.9900
X:72875328:CCAG:C	acceptor_gain	0.9900
X:72875329:CAGC:C	acceptor_gain	0.9900
X:72875330:AG:A	acceptor_gain	0.9900
X:72875331:GCTG:G	acceptor_loss	0.9900
X:72875332:CT:C	acceptor_loss	0.9900
X:72875333:T:C	acceptor_loss	0.9900
X:72875334:G:C	acceptor_gain	0.9900
X:72875623:ACACT:A	donor_loss	0.9900
X:72875624:CACTC:C	donor_loss	0.9900
X:72875625:ACTCA:A	donor_loss	0.9900

AlphaMissense

860 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:72873634:C:G	A128P	0.992
X:72873625:C:G	A131P	0.991
X:72873631:C:G	A129P	0.991
X:72873621:A:G	L132P	0.983
X:72873630:G:T	A129D	0.979
X:72873621:A:T	L132Q	0.975
X:72873612:A:G	L135P	0.960
X:72873639:A:G	L126P	0.955
X:72873618:A:G	L133P	0.954
X:72873621:A:C	L132R	0.953
X:72873652:A:G	W122R	0.918
X:72873652:A:T	W122R	0.918
X:72873633:G:T	A128D	0.911
X:72873612:A:T	L135Q	0.904
X:72873641:C:A	K125N	0.895
X:72873641:C:G	K125N	0.895
X:72873612:A:C	L135R	0.880
X:72873645:C:G	R124P	0.869
X:72873624:G:T	A131D	0.867
X:72873650:C:A	W122C	0.843
X:72873650:C:G	W122C	0.843
X:72873634:C:T	A128T	0.831
X:72873608:T:A	R136S	0.822
X:72873608:T:G	R136S	0.822
X:72873636:T:A	E127V	0.814
X:72873633:G:A	A128V	0.813
X:72873624:G:A	A131V	0.802
X:72873625:C:T	A131T	0.795
X:72873636:T:C	E127G	0.761
X:72873651:C:G	W122S	0.758

dbSNP variants (sampled 300 via entrez): RS1009689 (X:72930047 C>A), RS1009695 (X:72927633 C>T), RS1011193 (X:72915927 A>C,G,T), RS111548960 (X:72926302 G>A), RS112059343 (X:72907353 A>T), RS112101723 (X:72892210 A>G), RS112380080 (X:72879366 C>T), RS112387200 (X:72880028 G>C,T), RS112434114 (X:72895388 T>A), RS112465596 (X:72879155 T>G), RS112921015 (X:72896438 G>A), RS113082673 (X:72890261 C>T), RS113125255 (X:72936101 G>A), RS113621076 (X:72916249 G>A), RS113633812 (X:72909033 G>A)

Disease associations

OMIM: gene MIM:300878 | disease phenotypes: MIM:300882, MIM:193250

GenCC curated gene-disease

Mondo (2): Cornelia de Lange syndrome 5 (MONDO:0010471), volvulus of midgut (MONDO:0008666)

Orphanet (3): Cornelia de Lange syndrome (Orphanet:199), OBSOLETE: Familial intestinal malrotation-facial anomalies syndrome (Orphanet:2454), Familial intestinal malrotation (Orphanet:508410)

HPO phenotypes

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

GWAS associations

0 associations (top):

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
C562456	Volvulus Of Midgut (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Resveratrol	affects cotreatment, decreases expression	1
Atrazine	increases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Silicon Dioxide	decreases expression	1
Tretinoin	increases expression	1
Valproic Acid	increases methylation	1
Aflatoxin B1	decreases methylation	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT03356314	Not specified	COMPLETED	Prenatal Ultrasound Screening of Intestinal Malrotation With a Higher Risk of Volvulus