CABS1

Summary

CABS1 (calcium binding protein, spermatid associated 1, HGNC:30710) is a protein-coding gene on chromosome 4q13.3, encoding Calcium-binding and spermatid-specific protein 1 (Q96KC9). Calcium-binding protein.

Predicted to enable calcium ion binding activity. Predicted to be involved in flagellated sperm motility and spermatogenesis. Predicted to be located in acrosomal vesicle and sperm principal piece. Predicted to be active in mitochondrial inner membrane and motile cilium.

Source: NCBI Gene 85438 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 61 total
• MANE Select transcript: NM_033122

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:30710
Approved symbol	CABS1
Name	calcium binding protein, spermatid associated 1
Location	4q13.3
Locus type	gene with protein product
Status	Approved
Aliases	NYD-SP26, FLJ32897, CLPH
Ensembl gene	ENSG00000145309
Ensembl biotype	protein_coding
OMIM	618600
Entrez	85438

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000273936

RefSeq mRNA: 1 — MANE Select: NM_033122 NM_033122

CCDS: CCDS3539

Canonical transcript exons

ENST00000273936 — 2 exons

Exon	Start	End
ENSE00000969875	70334981	70336346
ENSE00000969876	70336966	70337116

Expression profiles

Bgee: expression breadth broad, 34 present calls, max score 99.37.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2080 / max 232.0322, expressed in 4 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
47914	0.1853	4
47913	0.0226	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
sperm	CL:0000019	99.37	gold quality
left testis	UBERON:0004533	95.77	gold quality
right testis	UBERON:0004534	94.64	gold quality
testis	UBERON:0000473	92.66	gold quality
adult organism	UBERON:0007023	86.02	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	84.03	gold quality
buccal mucosa cell	CL:0002336	61.63	silver quality
minor salivary gland	UBERON:0001830	59.08	gold quality
mouth mucosa	UBERON:0003729	56.63	gold quality
saliva-secreting gland	UBERON:0001044	55.75	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
cauda epididymis	UBERON:0004360	53.38	gold quality
epithelial cell of pancreas	CL:0000083	52.84	gold quality
myocardium	UBERON:0002349	50.25	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
quadriceps femoris	UBERON:0001377	46.26	gold quality
deltoid	UBERON:0001476	46.22	gold quality
tibialis anterior	UBERON:0001385	46.01	silver quality
vastus lateralis	UBERON:0001379	45.40	gold quality
ileal mucosa	UBERON:0000331	45.11	silver quality
pancreatic ductal cell	CL:0002079	45.06	silver quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
muscle tissue	UBERON:0002385	42.10	gold quality
nasal cavity mucosa	UBERON:0001826	41.44	gold quality
superficial temporal artery	UBERON:0001614	41.33	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-GEOD-134144	yes	31.79
E-ANND-3	no	1.96

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting CABS1, 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-574-5P	100.00	66.01	989
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-32-5P	99.98	75.21	1964
HSA-MIR-92A-3P	99.98	75.21	1960
HSA-MIR-92B-3P	99.98	75.25	1955
HSA-MIR-25-3P	99.98	74.60	1817
HSA-MIR-363-3P	99.98	74.72	1821
HSA-MIR-367-3P	99.98	74.83	1819
HSA-MIR-499A-5P	99.98	70.79	1323
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-1252-3P	99.55	67.71	2862
HSA-MIR-513A-3P	99.39	70.63	3620
HSA-MIR-513C-3P	99.39	70.63	3620
HSA-MIR-5580-5P	99.38	66.96	1139
HSA-MIR-3606-3P	99.11	69.84	3254
HSA-MIR-4699-5P	98.99	67.50	1210
HSA-MIR-12135	98.99	70.26	1814
HSA-MIR-520G-3P	98.91	67.38	1914
HSA-MIR-520H	98.91	67.38	1914
HSA-MIR-4709-3P	98.88	68.04	1594
HSA-MIR-6889-3P	98.84	67.35	1198
HSA-MIR-5197-3P	98.71	67.05	1905
HSA-MIR-6529-3P	98.68	66.76	1020
HSA-MIR-3689A-5P	98.35	70.12	1049
HSA-MIR-3689B-5P	98.35	70.12	1049
HSA-MIR-3689E	98.35	70.12	1049
HSA-MIR-3689F	98.35	70.08	1052
HSA-MIR-660-5P	98.16	68.27	680
HSA-MIR-4509	96.19	65.80	900

Literature-anchored findings (GeneRIF, showing 2)

• Human CABS1 has a peptide motif homologous to the anti-inflammatory peptide sequence of rat SMR1. (PMID:25632019)
• CABS1 is readily detected in human saliva and is associated with psychological and physiological indicators of stress. (PMID:28381457)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cabs1	ENSMUSG00000007907
rattus_norvegicus	Cabs1	ENSRNOG00000001950

Protein

Protein identifiers

Calcium-binding and spermatid-specific protein 1 — Q96KC9 (reviewed: Q96KC9)

Alternative names: Testis development protein NYD-SP26

All UniProt accessions (1): Q96KC9

UniProt curated annotations — full annotation on UniProt →

Function. Calcium-binding protein. Essential for maintaining the structural integrity of the sperm flagella.

Subcellular location. Cytoplasm. Mitochondrion inner membrane. Cell projection. Cilium. Flagellum. Cytoplasmic vesicle. Secretory vesicle. Acrosome.

RefSeq proteins (1): NP_149113* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026118	Ca-bd_spermatid	Family

Pfam: PF15367

UniProt features (11 total): modified residue 4, sequence variant 3, region of interest 2, chain 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q96KC9-F1	40.00	0.00

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 273, 287, 319, 376

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 47 (showing top): GOCC_SECRETORY_GRANULE, GOBP_MALE_GAMETE_GENERATION, chr4q13, MODULE_205, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOCC_MITOCHONDRIAL_ENVELOPE, ATTCTTT_MIR186, GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION, GOCC_SECRETORY_VESICLE, GOCC_MOTILE_CILIUM, GOCC_ORGANELLE_INNER_MEMBRANE, GOCC_SPERM_PRINCIPAL_PIECE, GOCC_ACROSOMAL_VESICLE, GOCC_CILIUM

GO Biological Process (2): spermatogenesis (GO:0007283), flagellated sperm motility (GO:0030317)

GO Molecular Function (1): calcium ion binding (GO:0005509)

GO Cellular Component (10): acrosomal vesicle (GO:0001669), mitochondrial inner membrane (GO:0005743), motile cilium (GO:0031514), sperm principal piece (GO:0097228), cytoplasm (GO:0005737), mitochondrion (GO:0005739), cilium (GO:0005929), membrane (GO:0016020), cytoplasmic vesicle (GO:0031410), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
cytoplasm	2
developmental process involved in reproduction	1
male gamete generation	1
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
metal ion binding	1
secretory granule	1
organelle inner membrane	1
mitochondrial membrane	1
cilium	1
sperm flagellum	1
intracellular anatomical structure	1
intracellular membrane-bounded organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
intracellular vesicle	1

Protein interactions and networks

STRING

422 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CABS1	SHCBP1L	Q9BZQ2	644
CABS1	LRCOL1	A6NCL2	581
CABS1	C20orf173	Q96LM9	581
CABS1	PRR27	Q6MZM9	543
CABS1	TMCO5A	Q8N6Q1	536
CABS1	SPMIP4	Q8N865	531
CABS1	SPATA31G1	Q5VYM1	507
CABS1	TTC21A	Q8NDW8	502
CABS1	ROPN1L	Q96C74	487
CABS1	ROPN1	Q9HAT0	484
CABS1	FAM229B	Q4G0N7	478
CABS1	CCDC187	A0A096LP49	476
CABS1	SMR3A	Q99954	470
CABS1	TMCO2	Q7Z6W1	470
CABS1	CAPZA3	Q96KX2	460

IntAct

4 interactions, top by confidence:

A	B	Type	Score
CABS1	TRAPPC10	psi-mi:“MI:0914”(association)	0.530
CABS1		psi-mi:“MI:0914”(association)	0.350
CABS1	ALOX12B	psi-mi:“MI:0914”(association)	0.350

BioGRID (31): TRAPPC4 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), C7orf43 (Affinity Capture-MS), TRAPPC9 (Affinity Capture-MS), TRAPPC5 (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS), TRAPPC2L (Affinity Capture-MS), TRAPPC3 (Affinity Capture-MS), TRAPPC1 (Affinity Capture-MS), C7orf43 (Affinity Capture-MS), TRAPPC10 (Affinity Capture-MS), TRAPPC9 (Affinity Capture-MS), TRAPPC4 (Affinity Capture-MS), TRAPPC2L (Affinity Capture-MS), TRAPPC2 (Affinity Capture-MS)

ESM2 similar proteins: A0JPP4, B7ZCC9, B9EKR1, E9Q7X6, J3KML8, O00592, O57604, P13611, P23471, P30005, P34910, P52549, P70628, Q01036, Q06093, Q1XI86, Q28858, Q2TA21, Q2TBJ9, Q3MIW9, Q3TNW5, Q3TYV2, Q5XI99, Q62059, Q62656, Q62781, Q68FD9, Q69558, Q6MG22, Q6R8J2, Q7TST5, Q80XH2, Q86TY3, Q8BT18, Q8BUE7, Q8C633, Q8IZF6, Q8N3K9, Q8VD58, Q8WXI7

Diamond homologs: Q2TBJ9, Q68FX6, Q8C633, Q95JW6, Q96KC9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	7
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

173 predictions. Top by Δscore:

Variant	Effect	Δscore
4:70336211:A:G	donor_gain	0.9900
4:70336156:G:GT	donor_gain	0.9600
4:70336201:G:GT	donor_gain	0.9600
4:70336210:GA:G	donor_gain	0.9000
4:70336211:A:AG	donor_gain	0.9000
4:70336241:G:T	donor_gain	0.8400
4:70336240:GGA:G	donor_gain	0.7900
4:70336042:G:GT	donor_gain	0.6500
4:70335883:G:T	donor_gain	0.6200
4:70335999:A:G	donor_gain	0.6200
4:70335919:G:GT	donor_gain	0.6100
4:70336157:A:T	donor_gain	0.6000
4:70336198:A:T	donor_gain	0.5900
4:70336390:TC:T	donor_gain	0.5900
4:70336431:GT:G	donor_gain	0.5900
4:70335883:G:GT	donor_gain	0.5600
4:70336180:GA:G	donor_gain	0.5600
4:70335955:G:GT	donor_gain	0.5500
4:70336250:T:TA	donor_gain	0.5400
4:70336251:A:AA	donor_gain	0.5400
4:70335766:GACC:G	donor_gain	0.5300
4:70335769:C:G	donor_gain	0.5300
4:70336121:G:GT	donor_gain	0.5200
4:70336215:G:GG	donor_gain	0.5000
4:70336248:T:G	donor_gain	0.5000
4:70336214:A:AG	donor_gain	0.4900
4:70336981:T:G	acceptor_gain	0.4800
4:70336181:A:G	donor_gain	0.4700
4:70336216:T:G	donor_gain	0.4500
4:70336971:A:C	acceptor_gain	0.4500

AlphaMissense

2601 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
4:70335841:T:C	F268L	0.976
4:70335843:T:A	F268L	0.976
4:70335843:T:G	F268L	0.976
4:70336006:T:C	F323L	0.959
4:70336008:C:A	F323L	0.959
4:70336008:C:G	F323L	0.959
4:70335986:C:A	A316D	0.929
4:70336186:T:C	F383L	0.919
4:70336188:T:A	F383L	0.919
4:70336188:T:G	F383L	0.919
4:70335842:T:C	F268S	0.918
4:70335985:G:C	A316P	0.918
4:70335994:T:C	S319P	0.914
4:70335434:T:C	L132S	0.899
4:70335217:T:C	F60L	0.892
4:70335219:T:A	F60L	0.892
4:70335219:T:G	F60L	0.892
4:70335842:T:G	F268C	0.891
4:70335980:T:C	L314P	0.886
4:70336007:T:C	F323S	0.876
4:70335428:T:A	V130D	0.874
4:70335839:T:A	V267E	0.874
4:70335848:T:C	L270P	0.860
4:70335980:T:A	L314H	0.847
4:70335442:T:C	F135L	0.845
4:70335444:T:A	F135L	0.845
4:70335444:T:G	F135L	0.845
4:70336000:T:G	Y321D	0.834
4:70335829:T:C	F264L	0.828
4:70335831:T:A	F264L	0.828

dbSNP variants (sampled 300 via entrez): RS1000533156 (4:70336416 GA>G,GAA,GAAA), RS1001089388 (4:70335870 C>A,T), RS1003859529 (4:70336286 A>T), RS1005502453 (4:70337544 A>T), RS1005879607 (4:70336334 G>T), RS1006326401 (4:70336578 A>G), RS1007129101 (4:70337264 A>G), RS1008833357 (4:70336224 T>C), RS1009144258 (4:70334588 A>G), RS1009790014 (4:70335076 C>A,T), RS1010096113 (4:70337058 A>G), RS1013470893 (4:70336651 A>G), RS1013661408 (4:70336901 T>G), RS1014133307 (4:70336359 C>T), RS1015419282 (4:70335674 T>C)

Disease associations

OMIM: gene MIM:618600 | 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: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression	2
CGP 52608	affects binding, increases reaction	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression, increases expression	1
dorsomorphin	increases expression, affects cotreatment, decreases expression	1
Vorinostat	affects cotreatment, increases expression	1
Benzo(a)pyrene	increases methylation, affects methylation	1
Aflatoxin B1	increases expression	1
Antirheumatic Agents	increases expression	1

Clinical trials (associated diseases)

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