CHST4, human gene | AUM BioTech

01 Summary and function

What CHST4 does

This gene encodes an N-acetylglucosamine 6-O sulfotransferase.

NCBI Gene summary

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Gene summary

This gene encodes an N-acetylglucosamine 6-O sulfotransferase. The encoded enzyme transfers sulfate from 3'phosphoadenosine 5'phospho-sulfate to the 6-hydroxyl group of N-acetylglucosamine on glycoproteins. This protein is localized to the Golgi and is involved in the modification of glycan structures on ligands of the lymphocyte homing receptor L-selectin. Alternate splicing in the 5' UTR results in multiple transcript variants that encode the same protein.

Provided by RefSeq, Oct 2009, through NCBI Gene. NCBI disclaimer

Protein function

Carbohydrate sulfotransferase 4, Q8NCG5

Sulfotransferase involved in SELL/L-selectin ligand biosynthesis pathway. Catalyzes the transfer of the sulfate group from 3'-phospho-5'-adenylyl sulfate (PAPS) onto the hydroxyl group at C-6 position of the non-reducing N-acetylglucosamine (GlcNAc) residue within O-linked mucin-type glycans. Contributes to generate sialyl 6-sulfo Lewis X determinant (also known as MECA-79 epitope) for SELL recognition, a prerequisite for continuous lymphocyte homing into peripheral lymph nodes and antigen immune surveillance (PubMed:10330415, PubMed:11439191, PubMed:11726653, PubMed:12107080). Transfers the sulfate group primarily on core 2 GlcNAcbeta1-6(Galbeta1-3)GalNAcalphaSer/Thr and extended core 1 GlcNAcbeta1-3Galbeta1-3GalNAcalphaSer/Thr based O-linked glycans on CD34 and GLYCAM1 peripheral node addressins (PNAds) expressed on the lumenal side of high endothelial venules (HEVs) (PubMed:11439191). The recognition of PNAds by SELL initiates a multistep process comprising tethering and rolling of blood lymphocytes on HEVs against the blood flow, followed by chemokine signaling, integrin-mediated lymphocyte adhesion onto endothelial cells and lymphocyte transendothelial migration. Modulates rolling velocity and differential T and B lymphocyte recruitment into peripheral lymph nodes, with a major role in B lymphocyte homing. Might be redundant in sulfation of MADCAM1 and lymphocyte trafficking to mesenteric lymph nodes (By similarity). Can also sulfonate core 3 GlcNAcbeta1-3GalNAc-R based glycans as well as GlcNAcbeta1-3Galbeta1-Glc, GlcNAcbeta1-6ManOMe and GlcNAcbeta1-2Man oligosaccharides, which might be ectopically expressed during tumorigenesis (PubMed:11439191, PubMed:11726653, PubMed:12107080)

NCBI Gene summary · NCBI Gene annotation RS_2025_08 · read 2026-09-25 ET · NCBI Gene 10164Data from NCBI, provided as is; NCBI's policies and disclaimers apply.
UniProtKB function · 2026_03 · read 2026-09-25 ET · UniProt Q8NCG5UniProt data are available under the Creative Commons Attribution 4.0 licence.

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02 Transcripts and isoforms

The RNA a design targets

2 RefSeq and 7 Ensembl transcripts on GRCh38.p14; MANE Select NM_001166395.2.

NCBI Datasets · Ensembl

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What this tells you

A gene is silenced through its RNA, so the transcript is the target, not the gene. The map draws the isoforms 5' to 3', with the coding sequence taller than the untranslated regions and the isoforms aligned on the genome, so an exon they share sits in one column. A gene with many isoforms, or whose isoforms carry thousands of exons, draws the reference ones first and says how many it is holding back; the rest are drawn when you ask for them.

A sequence in a region every isoform carries knocks the whole gene down; one in an exon only some isoforms carry is isoform-specific. The MANE Select transcript in human, or the RefSeq Select and Ensembl canonical transcripts in mouse and rat, is the usual reference for a design. Where the two catalogues disagree, both are shown and neither is preferred.

Placed on GRCh38.p14 (GCF_000001405.40). MANE Select marks the one transcript RefSeq and Ensembl agree is the reference for this gene.

RefSeq 2 transcripts

coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width

Genomic strand: plus. Drawn 5' to 3', so exon 1 sits at the left here and at the lowest coordinate on the chromosome.

MANE Select

scale

Drawn 5' to 3' from each transcript's exons as placed on the reference assembly; exon 1 is the 5' exon on the transcript's own strand. Exon blocks are to scale with each other; introns are drawn at one fixed width whatever their length, so the map is not to scale along the chromosome. Numbers are exon ranks along the strand; a rank is omitted where the exon is too narrow to carry it.

A window on one transcript

One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.

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Transcript

No transcript is chosen.

Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.

RefSeq transcripts of this gene
Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
NM_001166395.2matches ENST00000539698.4	transcript variant 2	protein coding	MANE Select	2	2,159 nt	386 aaNP_001159867.1	Ready in a moment
NM_005769.2matches ENST00000927526.1	transcript variant 1	protein coding	none	2	2,145 ntexons sum to 2,124 nt; the record carries 21 nt beyond them	386 aaNP_005760.1	Ready in a moment

NCBI Datasets, RefSeq transcripts · NCBI Datasets 18.37.0; GCF_000001405.40-RS_2025_08 · read 2026-09-25 ET · NCBI Gene 10164Data from NCBI, provided as is; NCBI's policies and disclaimers apply.

Ensembl 7 transcripts

coding sequence, tall
untranslated region, thin
non-coding exon
intron, fixed width

Genomic strand: plus. Drawn 5' to 3', so exon 1 sits at the left here and at the lowest coordinate on the chromosome.

A window on one transcript

One pixel of the map above stands for several bases, and a block too short to see is drawn wider than its own scale, so the map chooses a region and the sequence here chooses the window. Click an exon on a row of the map, or drag across a row; then set the exact start and end below.

These controls are ready in a moment.

Transcript

No transcript is chosen.

Once a window is chosen this panel shows its length, its G and C count as a percentage of that length, the letters it is made of, the exons it falls in, whether it crosses a junction, and its antisense strand.

Lengths are spliced lengths, as each source states them. Exon ranks follow the strand: on a minus-strand gene exon 1 has the highest genomic coordinate. Reference assembly for human: GRCh38.

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03 Expression by tissue

Where CHST4 is expressed

54 GTEx tissues; the highest median in Pancreas, 2.70 TPM.

GTEx

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04 Protein

The protein CHST4 encodes

386 residues, reviewed Q8NCG5; 8 entries from the member databases this page shows along the chain; mean pLDDT 90.5; no experimental structure at PDBe.

UniProt · InterPro · AlphaFold DB · PDBe

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05 Interactions

Proteins STRING associates with CHST4

The 25 highest-scoring STRING partners at or above a combined score of 0.4, of up to 25 asked for; NTAN1, CHST2, SELL lead.

STRING v12.0

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06 Pathways

Where CHST4 acts, as Reactome curates it

1 curated, 0 inferred Reactome pathways for Q8NCG5 in human, v97.

Reactome

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07 Disease associations

Diseases linked to CHST4

95 Open Targets disease associations; atrial fibrillation first, at 0.31.

Open Targets

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08 Variants

Classified variants of CHST4

ClinVar: 124 records for CHST4, 27 pathogenic or likely pathogenic.

ClinVar

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09 Constraint

How much variation CHST4 tolerates

pLI none and LOEUF none in gnomAD v4 (GRCh38), on ENST00000539698.4.

gnomAD

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10 Orthologs

The same gene in mouse, rat and human

Mouse Chst4 by 3 of 3 votes; rat Chst4 by 3 of 3 votes. RGD is not answering, so the ortholog list could not be shown. Try again later. Reference b8cc1fec-ae0.

Alliance · NCBI · Ensembl Compara

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11 MicroRNAs

MicroRNAs hosted within CHST4

No annotated microRNA lies within CHST4 in Ensembl release 116, on GRCh38.p14.

Ensembl · miRBase

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12 Long non-coding RNAs

Long non-coding RNAs at the CHST4 locus

1 long non-coding RNA gene overlaps CHST4 in Ensembl release 116, antisense, without a symbol.

Ensembl

Order against a long non-coding RNA

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13 Literature

Papers that mention CHST4

717 PubMed-indexed papers mention CHST4 at Europe PMC, newest first. Europe PMC ignores letter case, so the count also covers another species' symbol spelled with the same letters.

Europe PMC

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Accession	Name	Biotype	Labels	Exons	Spliced length	Protein	Sequence
ENST00000539698.4matches NM_001166395.2	CHST4-202	protein coding	MANE SelectEnsembl canonical	2	2,159 nt	386 aaENSP00000441204.3	Ready in a moment
ENST00001137525.1	CHST4-207	protein coding	none	2	5,655 nt	386 aaENSP00000813920.1	Ready in a moment
ENST00000338482.6	CHST4-201	protein coding	none	3	5,616 nt	386 aaENSP00000341206.5	Ready in a moment
ENST00000927527.2	CHST4-206	protein coding	none	2	5,514 nt	386 aaENSP00000597586.1	Ready in a moment
ENST00000927526.1	CHST4-205	protein coding	none	2	5,497 nt	386 aaENSP00000597585.1	Ready in a moment
ENST00000866592.2	CHST4-204	protein coding	none	2	5,423 nt	386 aaENSP00000536651.1	Ready in a moment
ENST00000572693.1	CHST4-203	retained intron	none	1	1,333 nt	none	Ready in a moment

CHST4

CHST4

What CHST4 does

The RNA a design targets

Where CHST4 is expressed

The protein CHST4 encodes

Proteins STRING associates with CHST4

Where CHST4 acts, as Reactome curates it

Diseases linked to CHST4

Classified variants of CHST4

How much variation CHST4 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within CHST4

Long non-coding RNAs at the CHST4 locus

Papers that mention CHST4

CHST4

What CHST4 does

Gene summary

Protein function

The RNA a design targets

RefSeq 2 transcripts

A window on one transcript

Ensembl 7 transcripts

A window on one transcript

Where CHST4 is expressed

The protein CHST4 encodes

Proteins STRING associates with CHST4

Where CHST4 acts, as Reactome curates it

Diseases linked to CHST4

Classified variants of CHST4

How much variation CHST4 tolerates

The same gene in mouse, rat and human

MicroRNAs hosted within CHST4

Long non-coding RNAs at the CHST4 locus

Papers that mention CHST4

From CHST4 to a sequence that silences it

Choose the region

Cover the isoforms you mean

Think across species early

Check expression in your model

Run the controls

Pick the product

Gene summary

Protein function

RefSeq 2 transcripts

A window on one transcript

Ensembl 7 transcripts

A window on one transcript