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How to read an HLA allele name, field by field

Updated 2026-10-29 · allele examples checked against IPD-IMGT/HLA 3.66.0 on 2026-10-29

An HLA allele name tells you the gene, then up to four numbered fields separated by colons, then sometimes a letter about expression. Each field answers a narrower question than the one before it: which allele group, which protein, which coding sequence, which full sequence including introns.

Read left to right, and stop as soon as you have the precision your question needs. Everything after that point is detail you can safely ignore for that question, and nothing before it can be dropped.

The parts of a name

Take HLA-A*02:01:01:01, a full four-field name.

The colons have been there since April 2010. Before that, the same allele was written A*01010101-style, with the fields run together. If you are reading older data, the guide on converting pre-2010 names covers that.

Field 1: the allele group

The digits before the first colon are the type. The naming page at hla.alleles.org says this "often corresponds to the serological antigen carried by an allotype". So HLA-DRB1*13 is a group of alleles that encode the DR13 antigen, or that share sequence homology with other DRB1*13 alleles.

"Often" matters. The same page describes DRB1*13 as alleles that encode the DR13 antigen or share sequence homology with other DRB1*13 alleles, so group membership does not by itself promise a serological equivalent. Some alleles in a group are not expressed at all: A*24:09N sits in the A*24 group and is a null allele.

A name with only one field, such as A*02, says almost nothing at allele level. In IPD-IMGT/HLA release 3.66.0 the A*02 group (written A*02:XX in some reports) covers 2,127 named alleles.

Field 2: the protein

The second field is numbered in the order the DNA sequences were determined. Two alleles that differ anywhere in the first two fields must differ by at least one nucleotide substitution that changes the amino acid sequence. Two-field resolution is therefore protein-level resolution.

That is why the CPIC pharmacogenomic guideline records, for example, key on two-field names such as B*57:01. It is also why a two-field name is still ambiguous at the sequence level. In release 3.66.0, A*02:01 covers 519 full-length alleles. They all encode the same protein, and they differ elsewhere.

Numbers in the second field are not capped at 99. The 2010 nomenclature update said that families reaching 100 alleles continue sequentially, and A*24:100 is an assigned name in release 3.66.0.

Field 3: synonymous coding differences

The third field separates alleles that encode the same protein but differ by a synonymous substitution inside the coding sequence. The naming page's own example is HLA-DRB1*13:01:02, which differs from DRB1*13:01:01 by a synonymous mutation.

You rarely need the third field to decide anything about the protein. You do need it to say exactly which sequence was observed, and some reporting codes depend on it. G groups, for example, are named with three fields (see G groups and P groups).

Field 4: introns and untranslated regions

The fourth field separates alleles that differ only outside the coding sequence: in introns, or in the 5' or 3' untranslated regions. HLA-DRB1*13:01:01:02 differs from DRB1*13:01:01:01 by a mutation outside the coding region.

Fourth-field differences usually come from full-gene sequencing. Most typing methods that read only the exons cannot see them, which is one reason a report's resolution and the name's length are different things. The guide on typing resolution separates the two.

Names are only as long as they need to be

Not every allele has four fields. The nomenclature rule is that all alleles receive at least a two-field name, and longer names are assigned only when necessary. A name gets a third field when a relative exists that encodes the same protein with a different coding sequence, and a fourth when a relative differs only outside the coding sequence.

That means a name can grow. In release 3.66.0, A*01:284 became A*01:284:01 because a second allele, A*01:284:02, was named alongside it. Nothing about the first allele's sequence changed; its neighbourhood did. Software that stores names as fixed-width strings, or that assumes the field count tells you the typing resolution, will get this wrong.

The expression suffix

A letter at the end records expression status when it is not normal. N marks a null allele that is not expressed, such as HLA-A*24:09N. L, S, C, A and Q mark low, secreted, cytoplasmic, aberrant and questionable expression. As of September 2026 no alleles have been named with C or A.

The suffix is part of the name. A*24:09N and a hypothetical A*24:09 are not the same allele, and dropping the N turns a non-expressed allele into an apparently expressed one. The suffixes guide covers each letter and the traps around them.

Names that look like alleles but are not

Several strings in HLA reports use allele-like syntax for something else:

• G and P group names end in G or P: A*02:01:01G and A*02:01P name sets of alleles, not one allele.
• Multiple allele codes put letters in the second field, as in A*02:AB. They are reporting shorthand for a list.
• The XX code, as in A*02:XX, stands for the whole first-field group.
• Antigen names such as A2 or DR4 have no asterisk. They are serological, not sequence-based.

When software meets one of these, it should know which kind it is looking at rather than treating it as an unknown allele.

How many alleles are there?

The September 2026 statistics page at hla.alleles.org lists 46,146 named HLA alleles: 31,311 class I and 14,835 class II. HLA-B alone has 11,328. New names arrive every quarter, because IPD-IMGT/HLA publishes a release each January, April, July and October.

That pace is why a name you learned five years ago may not be the current name, and why any check of an allele name has to say which release it was checked against.

Frequently asked questions

What does the asterisk mean in an HLA allele name?

It separates the gene from the allele designation and signals a sequence-defined allele. Serological antigen names such as A2 do not use it.

Is HLA-A*02:01 an allele?

It is a valid two-field name for a protein, and it covers many full-length alleles that encode that same protein: 519 of them in IPD-IMGT/HLA release 3.66.0. Whether that is precise enough depends on the question you are asking.

Do I need to write the HLA- prefix?

The prefix identifies the HLA region and is recommended in formats such as GL String. Many lab reports omit it, and tools generally accept both HLA-A*02:01 and A*02:01.

Why do some allele names have three fields and others four?

Names are only as long as needed to tell an allele apart from its nearest relatives. A field is added when a relative differs at that level, so the field count reflects the allele's neighbourhood, not how carefully it was typed.