CLN5

Chr 13q22.3

CLN5 lysosomal BMP synthase

MANE:: ENST00000377453.9

OMIM: 608102 ↗NCBI: 1203 ↗Ensembl ↗

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Predicted protein structure

AlphaFold predicted structure

CLN5 · O75503

v62025-08-01

Predicted Aligned Error matrix for CLN5 — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

82.3/ 100

Confident

358 residues

Confidence breakdown

Very high(≥ 90)64%
Confident(70–90)13%
Low(50–70)8%
Very low(< 50)15%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

Ataxia and cerebellar anomalies - narrow panel
BIALLELIC, autosomal or pseudoautosomal
Childhood onset dystonia, chorea or related movement disorder
BIALLELIC, autosomal or pseudoautosomal
DDG2P
BIALLELIC, autosomal or pseudoautosomal
Intellectual disability
BIALLELIC, autosomal or pseudoautosomal
Likely inborn error of metabolism
BIALLELIC, autosomal or pseudoautosomal
Lysosomal storage disorder
BIALLELIC, autosomal or pseudoautosomal
Neuronal ceroid lipofuscinosis
BIALLELIC, autosomal or pseudoautosomal
Retinal disorders
BIALLELIC, autosomal or pseudoautosomal

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Disease associations (Open Targets)

CLN5 disease
0.77
neuronal ceroid lipofuscinosis 5
0.77
neuronal ceroid lipofuscinosis
0.71
late infantile neuronal ceroid lipofuscinosis
0.59
intellectual disability, short stature, facial anomalies, and joint dislocations
0.48
hereditary disease
0.47
infantile neuronal ceroid lipofuscinosis
0.46
juvenile neuronal ceroid lipofuscinosis 5
0.37
adult neuronal ceroid lipofuscinosis 5
0.37
late infantile neuronal ceroid lipofuscinosis 5
0.37

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Bis(monoacylglycero)phosphate synthase CLN5

Catalyzes the synthesis of bis(monoacylglycero)phosphate (BMP) via transacylation of 2 molecules of lysophosphatidylglycerol (LPG) (PubMed:37708259). BMP also known as lysobisphosphatidic acid plays a key role in the formation of intraluminal vesicles and in maintaining intracellular cholesterol homeostasis (PubMed:37708259). Can use only LPG as the exclusive lysophospholipid acyl donor for base exchange and displays BMP synthase activity towards various LPGs (LPG 14:0, LPG 16:0, LPG 18:0, LPG 18:1) with a higher preference for longer chain lengths (PubMed:37708259). Plays a role in influencing the retrograde trafficking of lysosomal sorting receptors SORT1 and IGF2R from the endosomes to the trans-Golgi network by controlling the recruitment of retromer complex to the endosomal membrane (PubMed:22431521). Regulates the localization and activation of RAB7A which is required to recruit the retromer complex to the endosomal membrane (PubMed:22431521)