UniProtKB/SwissProt variant VAR

Variant information

Variant position:

163

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

Type of variant:

Disease [Disclaimer]

The variants are classified into three categories: Disease, Polymorphism and Unclassified.

Disease: Variants implicated in disease according to literature reports.
Polymorphism: Variants not reported to be implicated in disease.
Unclassified: Variants with uncertain implication in disease according to literature reports. Evidence against or in favor of a pathogenic role is limited and/or conflicting.

Residue change:

From Arginine (R) to Glutamine (Q) at position 163 (R163Q, p.Arg163Gln).

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 basic (R) to medium size and polar (Q)

The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:

1

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

Involvement in disease:

Neu-Laxova syndrome 1 (NLS1) [MIM:256520]: A lethal, autosomal recessive multiple malformation syndrome characterized by ichthyosis, marked intrauterine growth restriction, microcephaly, short neck, limb deformities, hypoplastic lungs, edema, and central nervous system anomalies including lissencephaly, cerebellar hypoplasia and/or abnormal/agenesis of the corpus callosum. Abnormal facial features include severe proptosis with ectropion, hypertelorism, micrognathia, flattened nose, and malformed ears. {ECO:0000269|PubMed:24836451}. Note=The disease is caused by mutations affecting the gene represented in this entry.

The name and a short description of the disease associated with the variant. For more information about the disease, the user can refer to OMIM, following the link provided after the disease acronym.

Variant description:

In NLS1.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs587777483 [ dbSNP | Ensembl ]

Sequence information

Variant position:

163

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

Protein sequence length:

533

The length of the canonical sequence.

Location on the sequence:

LNGKTLGILGLGRIGREVAT R MQSFGMKTIGYDPIISPEVS

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                         LNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVS

Chimpanzee                    LNGKTLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVS

Mouse                         LNGKTLGILGLGRIGREVATRMQSFGMKTVGYDPIISPEVA

Rat                           LNGKTLGILGLGRIGREVAARMQAFGMKTVGYDPIISPEVA

Pig                           LNGKVLGILGLGRIGREVATRMQSFGMKTIGYDPIIAPEVS

Bovine                        LNGKVLGILGLGRIGREVATRMQSFGMKTIGYDPIISPEVS

Slime mold                    IRGKTLGIIGYGHIGSQLSVLAEAMGMSVLYYD--IARRLP

Baker's yeast                 VRGKTLGIIGYGHIGSQLSVLAEAMGLHVLYYD--IVTIMA

Fission yeast                 IRGKTLGIIGYGHIGSQLSVLAEAMGLHVVYYD--ILPIMP

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.

Type	Positions	Description
Chain	2 – 533	D-3-phosphoglycerate dehydrogenase
Binding site	175 – 175	NAD
Helix	155 – 165

Literature citations

Neu-Laxova syndrome, an inborn error of serine metabolism, is caused by mutations in PHGDH.
Shaheen R.; Rahbeeni Z.; Alhashem A.; Faqeih E.; Zhao Q.; Xiong Y.; Almoisheer A.; Al-Qattan S.M.; Almadani H.A.; Al-Onazi N.; Al-Baqawi B.S.; Saleh M.A.; Alkuraya F.S.;
Am. J. Hum. Genet. 94:898-904(2014)
Cited for: INVOLVEMENT IN NLS1; VARIANTS NLS1 ARG-140 AND GLN-163;

UniProtKB/Swiss-Prot O43175: Variant p.Arg163Gln