UniProtKB/SwissProt variant VAR

tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1
Gene: PYROXD1
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Variant information Variant position:

155 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 Asparagine (N) to Serine (S) at position 155 (N155S, p.Asn155Ser). 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 medium size and polar (N) to small size and polar (S) 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
Variant description:

In MFM8; also found in a patient with limb-girdle muscular dystrophy; decreased NADPH dehydrogenase activity; decreased function in cellular response to oxidative stress; no effect on subcellular location in the nucleus and sarcomere. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs781565158 [ dbSNP | Ensembl ]

Sequence information Variant position:

155 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Protein sequence length:

500 The length of the canonical sequence.
Location on the sequence:

DSAQEFQKQLTKAKRIMIIG N GGIALELVYEIEGCEVIWAI 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                         DSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWAI

Mouse                         DSAQEFQKELAKARRIMIVGNGGIALELAYEIEGCEVVWAI

Rat                           DSAQEFQKQLTKARRIMIVGNGGIALELAYEVEVCEVIWAI

Bovine                        DSAQEFQKQLTKAKRIMIIGNGGIALELVYEIEGCEVIWVI

Zebrafish                     DSAQEFQKRLSTAKRIVVIGNGGIALELVYEVEGCEVIWAV

Drosophila                    DSVQLLQRKLATAKDVLILGNGGIASELAYELKDVNVHWVV

Slime mold                    ETIVDLKNRLSNAKRIVIVGNGGIALELIHEIKNCQIIWSI

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	1 – 500	tRNA ligase complex-associated NAD(P)H dehydrogenase PYROXD1
Binding site	157 – 157
Binding site	158 – 158

Literature citations
The oxidoreductase PYROXD1 uses NAD(P)+ as an antioxidant to sustain tRNA ligase activity in pre-tRNA splicing and unfolded protein response.
Asanovic I.; Strandback E.; Kroupova A.; Pasajlic D.; Meinhart A.; Tsung-Pin P.; Djokovic N.; Anrather D.; Schuetz T.; Suskiewicz M.J.; Sillamaa S.; Koecher T.; Beveridge R.; Nikolic K.; Schleiffer A.; Jinek M.; Hartl M.; Clausen T.; Penninger J.; Macheroux P.; Weitzer S.; Martinez J.;
Mol. Cell 81:2520-2532.e16(2021)
Cited for: X-RAY CRYSTALLOGRAPHY (3.20 ANGSTROMS) IN COMPLEX WITH FAD; FUNCTION; CATALYTIC ACTIVITY; COFACTOR; SUBUNIT; INTERACTION WITH RTCB; CHARACTERIZATION OF VARIANTS MFM8 SER-155 AND HIS-372; MUTAGENESIS OF ASN-155; TRP-376 AND HIS-410;
Variants in the oxidoreductase PYROXD1 cause early-onset myopathy with internalized nuclei and myofibrillar disorganization.
O'Grady G.L.; Best H.A.; Sztal T.E.; Schartner V.; Sanjuan-Vazquez M.; Donkervoort S.; Abath Neto O.; Sutton R.B.; Ilkovski B.; Romero N.B.; Stojkovic T.; Dastgir J.; Waddell L.B.; Boland A.; Hu Y.; Williams C.; Ruparelia A.A.; Maisonobe T.; Peduto A.J.; Reddel S.W.; Lek M.; Tukiainen T.; Cummings B.B.; Joshi H.; Nectoux J.; Brammah S.; Deleuze J.F.; Ing V.O.; Ramm G.; Ardicli D.; Nowak K.J.; Talim B.; Topaloglu H.; Laing N.G.; North K.N.; MacArthur D.G.; Friant S.; Clarke N.F.; Bryson-Richardson R.J.; Boennemann C.G.; Laporte J.; Cooper S.T.;
Am. J. Hum. Genet. 99:1086-1105(2016)
Cited for: SUBCELLULAR LOCATION; INVOLVEMENT IN MFM8; VARIANTS MFM8 SER-155 AND HIS-372; CHARACTERIZATION OF VARIANTS MFM8 SER-155 AND HIS-372;
The impact of PYROXD1 deficiency on cellular respiration and correlations with genetic analyses of limb-girdle muscular dystrophy in Saudi Arabia and Sudan.
Saha M.; Reddy H.M.; Salih M.; Estrella E.; Jones M.D.; Mitsuhashi S.; Cho K.A.; Suzuki-Hatano S.; Rizzo S.A.; Hamad M.H.; Mukhtar M.M.; Hamed A.A.; Elseed M.A.; Lek M.; Valkanas E.; MacArthur D.G.; Kunkel L.M.; Pacak C.A.; Draper I.; Kang P.B.;
Physiol. Genomics 50:929-939(2018)
Cited for: INVOLVEMENT IN LIMB-GIRDLE MUSCULAR DYSTROPHY; VARIANT SER-155; CHARACTERIZATION OF VARIANT SER-155;

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.

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q8WU10: Variant p.Asn155Ser