XNDC1N

Summary

XNDC1N (XRCC1 N-terminal domain containing 1, N-terminal like, HGNC:54661) is a protein-coding gene on chromosome 11q13.4, encoding Protein XNDC1N (Q6ZNB5).

Predicted to enable damaged DNA binding activity. Predicted to be involved in single strand break repair. Located in chromosome and nucleolus.

Source: NCBI Gene 100133315 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 8 total
• Druggable target: yes
• MANE Select transcript: NM_001375847

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:54661
Approved symbol	XNDC1N
Name	XRCC1 N-terminal domain containing 1, N-terminal like
Location	11q13.4
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000254469
Ensembl biotype	protein_coding
Entrez	100133315

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 10 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000528184, ENST00000528511, ENST00000528560, ENST00000529513, ENST00000529844, ENST00000531488, ENST00000532852, ENST00000533047, ENST00000534704, ENST00000679412, ENST00000679695, ENST00000862358

RefSeq mRNA: 2 — MANE Select: NM_001375847 NM_001375847, NM_001375848

CCDS: CCDS91528

Canonical transcript exons

ENST00000679412 — 6 exons

Exon	Start	End
ENSE00002149759	71916074	71916252
ENSE00002155908	71917621	71917776
ENSE00002174618	71918885	71919026
ENSE00002175076	71923309	71923475
ENSE00003912739	71928365	71928594
ENSE00003913835	71880704	71884621

Expression profiles

Bgee: expression breadth ubiquitous, 178 present calls, max score 91.91.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
buccal mucosa cell	CL:0002336	91.91	silver quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	86.19	gold quality
pancreatic ductal cell	CL:0002079	82.29	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	79.71	gold quality
calcaneal tendon	UBERON:0003701	77.19	gold quality
bone marrow cell	CL:0002092	76.30	gold quality
sural nerve	UBERON:0015488	76.17	gold quality
granulocyte	CL:0000094	75.31	gold quality
ileal mucosa	UBERON:0000331	74.67	silver quality
adrenal tissue	UBERON:0018303	74.27	gold quality
upper arm skin	UBERON:0004263	74.01	gold quality
left ovary	UBERON:0002119	73.24	gold quality
right ovary	UBERON:0002118	73.06	gold quality
ventricular zone	UBERON:0003053	73.01	gold quality
kidney epithelium	UBERON:0004819	72.80	gold quality
rectum	UBERON:0001052	72.72	gold quality
popliteal artery	UBERON:0002250	72.19	gold quality
tibial artery	UBERON:0007610	72.17	gold quality
left lobe of thyroid gland	UBERON:0001120	72.00	gold quality
mucosa of transverse colon	UBERON:0004991	71.94	gold quality
oviduct epithelium	UBERON:0004804	71.82	silver quality
metanephros cortex	UBERON:0010533	71.79	gold quality
right adrenal gland cortex	UBERON:0035827	71.66	gold quality
tonsil	UBERON:0002372	71.56	gold quality
right adrenal gland	UBERON:0001233	71.24	gold quality
colonic epithelium	UBERON:0000397	71.21	gold quality
thyroid gland	UBERON:0002046	71.21	gold quality
ganglionic eminence	UBERON:0004023	71.07	gold quality
smooth muscle tissue	UBERON:0001135	71.05	gold quality
left adrenal gland cortex	UBERON:0035825	71.04	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.08

Regulation

Is transcription factor: no

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	xndc1	ENSDARG00000032263
mus_musculus	Xndc1	ENSMUSG00000099481
drosophila_melanogaster	XRCC1	FBGN0026751

Paralogs (1): XRCC1 (ENSG00000073050)

Protein

Protein identifiers

Protein XNDC1N — Q6ZNB5 (reviewed: Q6ZNB5)

Alternative names: XRCC1 N-terminal domain-containing 1 N-terminal like

All UniProt accessions (9): A0A7P0TB54, A0A7P0Z4L6, E9PIP4, E9PJ82, E9PLZ0, E9PP57, Q6ZNB5, E9PQ18, H0YEW9

Isoforms (2)

UniProt ID	Names	Canonical?
Q6ZNB5-1	1	yes
Q6ZNB5-2	2

RefSeq proteins (2): NP_001362776, NP_001362777 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR002706	Xrcc1_N	Domain
IPR008979	Galactose-bd-like_sf	Homologous_superfamily

Pfam: PF01834

UniProt features (3 total): splice variant 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6ZNB5-F1	76.31	0.48

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 33 (showing top): chr11q13, GOBP_DNA_DAMAGE_RESPONSE, GOCC_NUCLEOLUS, GOBP_DNA_METABOLIC_PROCESS, GOBP_DNA_REPAIR, GOBP_SINGLE_STRAND_BREAK_REPAIR, ZWANG_DOWN_BY_2ND_EGF_PULSE, ALKBH3_TARGET_GENES, ARID5B_TARGET_GENES, ASH1L_TARGET_GENES, BANP_TARGET_GENES, DACH1_TARGET_GENES, ELF2_TARGET_GENES, HAND1_TARGET_GENES, KAT2A_TARGET_GENES

GO Biological Process (1): single strand break repair (GO:0000012)

GO Molecular Function (1): damaged DNA binding (GO:0003684)

GO Cellular Component (3): chromosome (GO:0005694), nucleolus (GO:0005730), nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intracellular membraneless organelle	2
DNA repair	1
DNA binding	1
nuclear lumen	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

266 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
XNDC1N	CNGA2	Q16280	287
XNDC1N	ATE1	O95260	271
XNDC1N	STIM1	Q13586	245
XNDC1N	TRPV2	Q9Y5S1	232
XNDC1N	TRPV4	Q9HBA0	215
XNDC1N	TRPA1	O75762	207
XNDC1N	ITPR1	Q14643	205
XNDC1N	PENK	P01210	204
XNDC1N	STIM2	Q9P246	195
XNDC1N	DLGAP1	P78335	185
XNDC1N	OR52A1	Q9UKL2	180
XNDC1N	OR52A5	Q9H2C5	180
XNDC1N	SLC18A3	Q16572	174
XNDC1N	DCLK1	O15075	166
XNDC1N	TRPM6	Q9BX84	166
XNDC1N	CNPY3	Q9BT09	166

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A0G2JV04, A2AP18, A7UA95, A9JTG5, D2H8V8, D2HNY3, D3Z8X7, E6ZIJ1, E7FCN8, F6QZ15, O60308, O75038, O77682, O94941, P54369, P54370, P57075, P70218, Q09M05, Q13322, Q14B46, Q4KLY6, Q4U2V3, Q58D13, Q5E9N9, Q5QNQ6, Q5RGE5, Q68DX3, Q68G58, Q69ZT1, Q6P5E6, Q6P9Q4, Q6ZNB5, Q80V31, Q8BMI3, Q8C5V5, Q8C6B2, Q8C7W7, Q925F4, Q92918

Diamond homologs: O54935, P18887, P32372, Q24JK4, Q60596, Q6ZNB5, Q9ESZ0, Q9R244, Q9R283, O18784, O35119, O62826, O62852, P19334, P34586, P48994, P48995, P79100, Q13507, Q61056, Q61143, Q9HCX4, Q9JMI9, Q9MYV9, Q9MYW0, Q9QUQ5, Q9QX01, Q9QX29, Q9QZC1, Q9TUN9, Q9UBN4, Q9UL62, Q9VJJ7, Q9WVC5, Q9Y210

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

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

Top pathogenic / likely-pathogenic (0)

SpliceAI

1688 predictions. Top by Δscore:

Variant	Effect	Δscore
11:71923326:C:CT	donor_gain	1.0000
11:71878511:G:GG	donor_gain	0.9900
11:71901864:C:CT	acceptor_gain	0.9900
11:71901865:A:C	acceptor_gain	0.9900
11:71916249:TCAA:T	acceptor_gain	0.9900
11:71916250:C:CT	acceptor_gain	0.9900
11:71916250:CAA:C	acceptor_gain	0.9900
11:71916251:A:T	acceptor_gain	0.9900
11:71916253:C:CC	acceptor_gain	0.9900
11:71916255:C:CT	acceptor_gain	0.9900
11:71916256:A:T	acceptor_gain	0.9900
11:71917620:CCAT:C	donor_gain	0.9900
11:71917655:C:A	donor_gain	0.9900
11:71923327:C:CT	donor_gain	0.9900
11:71928478:T:TA	donor_gain	0.9900
11:71884403:A:AG	acceptor_gain	0.9800
11:71916069:CATA:C	donor_loss	0.9800
11:71916070:ATACC:A	donor_loss	0.9800
11:71916071:TA:T	donor_loss	0.9800
11:71916072:A:AG	donor_loss	0.9800
11:71917654:T:TA	donor_gain	0.9800
11:71923395:T:TA	donor_gain	0.9800
11:71927879:C:A	donor_gain	0.9800
11:71928358:C:A	donor_gain	0.9800
11:71928422:ATTCT:A	donor_gain	0.9800
11:71884404:A:G	acceptor_gain	0.9700
11:71916068:ACAT:A	donor_loss	0.9700
11:71916251:AA:A	acceptor_gain	0.9700
11:71918884:CCCA:C	donor_gain	0.9700
11:71923325:A:AC	donor_gain	0.9700

AlphaMissense

1525 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:71884467:G:C	C40S	0.981
11:71884518:G:C	C57S	0.974
11:71884518:G:A	C57Y	0.969
11:71884515:G:C	C56S	0.963
11:71884497:G:C	C50S	0.961
11:71884497:G:A	C50Y	0.960
11:71884498:T:G	C50W	0.956
11:71884519:C:G	C57W	0.955
11:71923318:A:C	F12L	0.952
11:71923318:A:T	F12L	0.952
11:71923320:A:G	F12L	0.952
11:71884468:C:G	C40W	0.949
11:71884455:G:C	C36S	0.946
11:71884515:G:A	C56Y	0.946
11:71884516:C:G	C56W	0.946
11:71884518:G:T	C57F	0.945
11:71884467:G:T	C40F	0.944
11:71884467:G:A	C40Y	0.943
11:71884479:A:T	E44V	0.939
11:71884456:C:G	C36W	0.937
11:71884480:A:C	E44D	0.925
11:71884480:A:T	E44D	0.925
11:71884455:G:A	C36Y	0.917
11:71884497:G:T	C50F	0.914
11:71884494:A:G	Y49C	0.907
11:71884515:G:T	C56F	0.907
11:71884455:G:T	C36F	0.892
11:71916155:A:C	F178L	0.891
11:71916155:A:T	F178L	0.891
11:71916157:A:G	F178L	0.891

dbSNP variants (sampled 300 via entrez): RS1000010351 (11:71895947 C>G), RS1000019769 (11:71865328 T>G), RS1000039173 (11:71887069 G>C), RS1000087499 (11:71899944 T>C), RS1000121397 (11:71910949 C>A), RS1000152320 (11:71910790 C>A), RS1000233607 (11:71913663 G>A,T), RS1000274231 (11:71885751 T>C), RS1000282851 (11:71891975 G>A), RS1000350018 (11:71926579 T>C), RS1000383547 (11:71888845 G>A,T), RS1000523296 (11:71899729 C>G,T), RS1000662582 (11:71886143 T>A), RS1000719516 (11:71915974 CGTGT>C,CGT,CGTGTGT), RS1000782649 (11:71914875 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

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: yes

ChEMBL targets (1): CHEMBL3721310 (SINGLE PROTEIN)

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

CTD chemical–gene interactions

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Niclosamide	decreases expression	1

ChEMBL screening assays

1 unique, capped per target: 1 functional

Representative assays (with source publication via chembl_document):

Assay ID	Type	Description	Source paper
CHEMBL3734577	Functional	Inhibition of TRPC2 (unknown origin) expressed in HEK293 cells assessed as effect on agonist-induced Ca2+ changes	Agents and methods for treating ischemic and other diseases

Clinical trials (associated diseases)

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