LRRC72

Summary

LRRC72 (leucine rich repeat containing 72, HGNC:42972) is a protein-coding gene on chromosome 7p21.1, encoding Leucine-rich repeat-containing protein 72 (A6NJI9).

At a glance

• Clinical variants (ClinVar): 48 total — 1 pathogenic
• MANE Select transcript: NM_001195280

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:42972
Approved symbol	LRRC72
Name	leucine rich repeat containing 72
Location	7p21.1
Locus type	gene with protein product
Status	Approved
Aliases	CFAP279, FAP279
Ensembl gene	ENSG00000205858
Ensembl biotype	protein_coding
Entrez	100506049

Gene structure

Transcript identifiers

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

ENST00000382124, ENST00000401542, ENST00000482711

RefSeq mRNA: 1 — MANE Select: NM_001195280 NM_001195280

CCDS: CCDS56464

Canonical transcript exons

ENST00000401542 — 9 exons

Exon	Start	End
ENSE00001491000	16580074	16580101
ENSE00001563772	16581324	16581568
ENSE00001603645	16566313	16566402
ENSE00001616029	16537627	16537696
ENSE00001659617	16558889	16558999
ENSE00001704300	16557360	16557441
ENSE00001789244	16567391	16567543
ENSE00002223036	16526825	16527042
ENSE00003690757	16532495	16532568

Expression profiles

Bgee: expression breadth broad, 21 present calls, max score 96.90.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0133 / max 10.3750, expressed in 4 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
77319	0.0133	4

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	96.90	gold quality
left testis	UBERON:0004533	69.47	gold quality
right testis	UBERON:0004534	68.48	gold quality
testis	UBERON:0000473	66.77	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	65.27	gold quality
tibialis anterior	UBERON:0001385	63.68	silver quality
myocardium	UBERON:0002349	59.65	gold quality
pancreatic ductal cell	CL:0002079	58.91	silver quality
ileal mucosa	UBERON:0000331	58.73	silver quality
sperm	CL:0000019	55.97	gold quality
kidney epithelium	UBERON:0004819	55.25	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.87	gold quality
epithelial cell of pancreas	CL:0000083	54.52	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
quadriceps femoris	UBERON:0001377	49.73	gold quality
vastus lateralis	UBERON:0001379	48.28	gold quality
tendon of biceps brachii	UBERON:0008188	47.82	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
skin of hip	UBERON:0001554	46.80	silver quality
lateral nuclear group of thalamus	UBERON:0002736	45.38	gold quality
granulocyte	CL:0000094	44.58	silver quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
pharyngeal mucosa	UBERON:0000355	42.81	gold quality
gingival epithelium	UBERON:0001949	42.74	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
esophagus squamous epithelium	UBERON:0006920	41.88	gold quality
buccal mucosa cell	CL:0002336	41.47	gold quality
gingiva	UBERON:0001828	41.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	3.57

Regulation

Is transcription factor: no

Cross-species orthologs

0 orthologs

Paralogs (2): SNRPA1 (ENSG00000131876), LRMDA (ENSG00000148655)

Protein

Protein identifiers

Leucine-rich repeat-containing protein 72 — A6NJI9 (reviewed: A6NJI9)

All UniProt accessions (2): A6NJI9, F8VSY1

UniProt curated annotations — full annotation on UniProt →

RefSeq proteins (1): NP_001182209* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001611	Leu-rich_rpt	Repeat
IPR032675	LRR_dom_sf	Homologous_superfamily
IPR042655	LRC72	Family

Pfam: PF14580

UniProt features (6 total): repeat 4, chain 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NJI9-F1	79.40	0.37

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 22 (showing top): GSE27786_CD4_TCELL_VS_NEUTROPHIL_DN, GSE27786_NKCELL_VS_NEUTROPHIL_DN, GSE27786_NKTCELL_VS_NEUTROPHIL_UP, GSE34205_RSV_VS_FLU_INF_INFANT_PBMC_UP, GSE36392_TYPE_2_MYELOID_VS_EOSINOPHIL_IL25_TREATED_LUNG_DN, GSE7460_FOXP3_MUT_VS_HET_ACT_TCONV_DN, GSE2585_CTEC_VS_THYMIC_DC_UP, GSE2585_AIRE_KO_VS_WT_CD80_HIGH_MTEC_DN, IWANAGA_CARCINOGENESIS_BY_KRAS_PTEN_DN, chr7p21, GSE4535_BM_DERIVED_DC_VS_FOLLICULAR_DC_UP, GSE5455_HEALTHY_VS_TUMOR_BEARING_MOUSE_SPLEEN_MONOCYTE_UP, GSE5455_HEALTHY_VS_TUMOR_BEARING_MOUSE_SPLEEN_MONOCYTE_24H_INCUBATION_DN, GSE5099_UNSTIM_VS_MCSF_TREATED_MONOCYTE_DAY7_UP, GSE5099_MONOCYTE_VS_ALTERNATIVE_M2_MACROPHAGE_UP

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1

Protein interactions and networks

STRING

370 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRRC72	ANKMY2	Q8IV38	608
LRRC72	CFAP92	Q9ULG3	514
LRRC72	TMEM248	Q9NWD8	474
LRRC72	CCDC116	Q8IYX3	452
LRRC72	IQUB	Q8NA54	452
LRRC72	AARD	Q4LEZ3	448
LRRC72	SPMIP9	Q96LM6	447
LRRC72	ARL10	Q8N8L6	447
LRRC72	CRPPA	A4D126	441
LRRC72	PLPP6	Q8IY26	430
LRRC72	TMEM256	Q8N2U0	423
LRRC72	DHRSX	Q8N5I4	420
LRRC72	BZW2	Q9Y6E2	417
LRRC72	RNF32	Q9H0A6	405
LRRC72	CCDC180	Q9P1Z9	400

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0JM56, A0M8T3, A1X154, A4D7T3, A6NJI9, Q008S8, Q00PJ3, Q07DV3, Q07DX6, Q07DY6, Q07DZ7, Q07E17, Q07E30, Q07E43, Q09YH1, Q09YI3, Q09YJ5, Q09YK6, Q09YN0, Q0VD31, Q108U1, Q2IBB1, Q2IBB4, Q2IBE3, Q2IBF5, Q2IBG0, Q2QL84, Q2QLA4, Q2QLB5, Q2QLC6, Q2QLG0, Q2QLH1, Q32NR9, Q5PPX0, Q5ZLG9, Q6DCF6, Q6GQN5, Q6PJI9, Q6ZRR7, Q8BH70

Diamond homologs: A6H759, A6NJI9, P09661, P57784, Q4R8Y8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	41
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
583954	NC_000007.14:g.(?16308523)(16689906_?)del	Pathogenic

SpliceAI

1606 predictions. Top by Δscore:

Variant	Effect	Δscore
7:16527038:GCCGG:G	donor_gain	1.0000
7:16527039:CCGGG:C	donor_loss	1.0000
7:16527041:GG:G	donor_gain	1.0000
7:16527042:GG:G	donor_gain	1.0000
7:16527042:GGTA:G	donor_loss	1.0000
7:16527043:G:C	donor_loss	1.0000
7:16527043:G:GG	donor_gain	1.0000
7:16527044:T:TC	donor_loss	1.0000
7:16558992:GATCC:G	donor_gain	1.0000
7:16558996:C:CG	donor_gain	1.0000
7:16558996:C:G	donor_gain	1.0000
7:16559000:G:GG	donor_gain	1.0000
7:16566307:TTGCA:T	acceptor_loss	1.0000
7:16566308:TGCAG:T	acceptor_loss	1.0000
7:16566309:GCAGG:G	acceptor_loss	1.0000
7:16566310:CAGGT:C	acceptor_loss	1.0000
7:16566311:A:AC	acceptor_loss	1.0000
7:16566403:G:GG	donor_gain	1.0000
7:16580102:G:GG	donor_gain	1.0000
7:16581320:GCAGA:G	acceptor_loss	1.0000
7:16581321:CAGAA:C	acceptor_loss	1.0000
7:16581322:A:AG	acceptor_gain	1.0000
7:16581323:G:GA	acceptor_gain	1.0000
7:16581323:GA:G	acceptor_gain	1.0000
7:16581323:GAA:G	acceptor_gain	1.0000
7:16581323:GAAC:G	acceptor_gain	1.0000
7:16581323:GAACT:G	acceptor_gain	1.0000
7:16536453:C:G	donor_gain	0.9900
7:16558966:G:GT	donor_gain	0.9900
7:16558976:G:T	donor_gain	0.9900

AlphaMissense

1872 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
7:16537668:T:C	L69S	0.972
7:16557412:T:C	L96P	0.971
7:16557406:T:C	L94P	0.966
7:16566326:T:A	N147K	0.962
7:16566326:T:G	N147K	0.962
7:16537683:T:C	L74P	0.959
7:16537677:T:C	L72S	0.957
7:16537683:T:A	L74H	0.956
7:16537658:T:C	F66L	0.955
7:16537660:T:A	F66L	0.955
7:16537660:T:G	F66L	0.955
7:16537693:C:A	N77K	0.952
7:16537693:C:G	N77K	0.952
7:16558919:T:C	L116P	0.952
7:16557422:T:A	N99K	0.951
7:16557422:T:G	N99K	0.951
7:16557427:T:A	I101K	0.950
7:16537692:A:T	N77I	0.948
7:16557406:T:A	L94Q	0.947
7:16532553:T:C	L50P	0.944
7:16557375:T:C	F84L	0.939
7:16557377:T:A	F84L	0.939
7:16557377:T:G	F84L	0.939
7:16558997:T:C	L142P	0.939
7:16537683:T:G	L74R	0.938
7:16566373:T:C	L163P	0.938
7:16566324:A:G	N147D	0.937
7:16558935:T:A	N121K	0.936
7:16558935:T:G	N121K	0.936
7:16537659:T:C	F66S	0.935

dbSNP variants (sampled 300 via entrez): RS1000042391 (7:16536670 A>G,T), RS1000044380 (7:16539208 C>G,T), RS1000058130 (7:16568845 C>A), RS1000064028 (7:16531675 C>G), RS1000099471 (7:16550368 C>T), RS1000107088 (7:16568655 G>A), RS1000167486 (7:16533985 T>G), RS1000197973 (7:16533703 T>C), RS1000229894 (7:16571456 A>C,G), RS1000239874 (7:16563375 T>C), RS1000309700 (7:16565863 C>A,T), RS1000355689 (7:16525943 C>A), RS1000423722 (7:16558197 C>G), RS1000432957 (7:16528098 G>T), RS1000651077 (7:16553282 T>C,G)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:614643, MIM:616052

GenCC curated gene-disease

Mondo (2): muscular dystrophy-dystroglycanopathy (congenital with brain and eye anomalies), type A, 7 (MONDO:0013835), autosomal recessive limb-girdle muscular dystrophy type 2U (MONDO:0014474)

Orphanet (2): ISPD-related limb-girdle muscular dystrophy R20 (Orphanet:352479), Walker-Warburg syndrome (Orphanet:899)

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

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

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

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT05989620	Not specified	RECRUITING	Long-Term Development of Muscular Dystrophy Outcome Assessments