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UniProtKB/Swiss-Prot Q10471: Variant p.Phe104Ser

Polypeptide N-acetylgalactosaminyltransferase 2
Gene: GALNT2
Variant information

Variant position:  104
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Type of variant:  LP/P [Disclaimer]
The variants are classified into three categories: LP/P, LB/B and US.
  • LP/P: likely pathogenic or pathogenic.
  • LB/B: likely benign or benign.
  • US: uncertain significance

Residue change:  From Phenylalanine (F) to Serine (S) at position 104 (F104S, p.Phe104Ser).
Indicates the amino acid change of the variant. The one-letter and three-letter codes for amino acids used in UniProtKB/Swiss-Prot are those adopted by the commission on Biochemical Nomenclature of the IUPAC-IUB.

Physico-chemical properties:  Change from large size and aromatic (F) to small size and polar (S)
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -2
The score within a Blosum matrix for the corresponding wild-type to variant amino acid change. The log-odds score measures the logarithm for the ratio of the likelihood of two amino acids appearing by chance. The Blosum62 substitution matrix is used. This substitution matrix contains scores for all possible exchanges of one amino acid with another:
  • Lowest score: -4 (low probability of substitution).
  • Highest score: 11 (high probability of substitution).
More information can be found on the following page

Variant description:  In CDG2T; loss-of-funtion variant resulting in lack of ApoC-III and IgA1 glycosylation.
Any additional useful information about the variant.



Sequence information

Variant position:  104
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  571
The length of the canonical sequence.

Location on the sequence:   EAYVGGTMVRSGQDPYARNK  F NQVESDKLRMDRAIPDTRHD
The residue change on the sequence. Unless the variant is located at the beginning or at the end of the protein sequence, both residues upstream (20) and downstream (20) of the variant will be shown.

Residue conservation: 
The multiple alignment of the region surrounding the variant against various orthologous sequences.

Human                         EAYVGGTMVRSGQDPYARNKFNQVESDKLRMDRAIPDTRHD

Mouse                         EAYVGGTMVRSGQDPYARNKFNQVESDKLHMDRGIPDTRHD

Drosophila                    AGYIRAGALRNGEDPYIRNRFNQEASDALPSNRDIPDTRNP

Sequence annotation in neighborhood:  
The regions or sites of interest surrounding the variant. In general the features listed are posttranslational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. The "Sequence annotation in neighborhood" lines have a fixed format:
  • Type: the type of sequence feature.
  • Positions: endpoints of the sequence feature.
  • Description: contains additional information about the feature.

TypePositionsDescription
Chain 1 – 571 Polypeptide N-acetylgalactosaminyltransferase 2
Chain 52 – 571 Polypeptide N-acetylgalactosaminyltransferase 2 soluble form
Topological domain 25 – 571 Lumenal


Literature citations

Loss of function of GALNT2 lowers high-density lipoproteins in humans, nonhuman primates, and rodents.
Khetarpal S.A.; Schjoldager K.T.; Christoffersen C.; Raghavan A.; Edmondson A.C.; Reutter H.M.; Ahmed B.; Ouazzani R.; Peloso G.M.; Vitali C.; Zhao W.; Somasundara A.V.; Millar J.S.; Park Y.; Fernando G.; Livanov V.; Choi S.; Noe E.; Patel P.; Ho S.P.; Kirchgessner T.G.; Wandall H.H.; Hansen L.; Bennett E.P.; Vakhrushev S.Y.; Saleheen D.; Kathiresan S.; Brown C.D.; Abou Jamra R.; LeGuern E.; Clausen H.; Rader D.J.;
Cell Metab. 24:234-245(2016)
Cited for: VARIANTS CDG2T SER-104 AND 289-GLN--GLN-571 DEL; CHARACTERIZATION OF VARIANTS CDG2T SER-104 AND 289-GLN--GLN-571 DEL; INVOLVEMENT IN CDG2T; FUNCTION;

Disclaimer: Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. They are not in any way intended to be used as a substitute for professional medical advice, diagnostic, treatment or care.