UniProtKB/Swiss-Prot Q8NHU3: Variant p.Ile62Ser

Phosphatidylcholine:ceramide cholinephosphotransferase 2
Gene: SGMS2
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Variant information Variant position:

62 The position of the amino-acid change on the UniProtKB canonical protein sequence.
Type of variant:

US 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 Isoleucine (I) to Serine (S) at position 62 (I62S, p.Ile62Ser). 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 hydrophobic (I) 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 CDLSMD; uncertain significance; no effect on enzymatic activity; does not localize to plasma membrane; accumulates in the endoplasmic reticulum. Any additional useful information about the variant.

Sequence information Variant position:

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

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

PKSLSSGLRKGTKKYPDYIQ I AMPTESRNKFPLEWWKTGIA 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                         PKSLSSGLRKGTKKYPDYIQIAMPTESRNKFPLEWWKTGIA

Mouse                         PKTLSNGLRKGAKKYPDYIQISMPNDSKNKFPLEWWKTGIA

Rat                           PKTLSNGLRKGAKKYPDYIQISMPNDSRNKLPLEWWKTGIA

Caenorhabditis elegans        PTPIRKEF-----TCEDTFHHEHHGNSEG------FKTLTA

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 – 365	Phosphatidylcholine:ceramide cholinephosphotransferase 2

Literature citations
Osteoporosis and skeletal dysplasia caused by pathogenic variants in SGMS2.
Pekkinen M.; Terhal P.A.; Botto L.D.; Henning P.; Maekitie R.E.; Roschger P.; Jain A.; Kol M.; Kjellberg M.A.; Paschalis E.P.; van Gassen K.; Murray M.; Bayrak-Toydemir P.; Magnusson M.K.; Jans J.; Kausar M.; Carey J.C.; Somerharju P.; Lerner U.H.; Olkkonen V.M.; Klaushofer K.; Holthuis J.C.; Maekitie O.;
JCI Insight 4:0-0(2019)
Cited for: FUNCTION; SUBCELLULAR LOCATION; INVOLVEMENT IN CDL; INVOLVEMENT IN CDLSMD; VARIANT CDL 50-ARG--THR-365 DEL; VARIANTS CDLSMD SER-62 AND ARG-64; CHARACTERIZATION OF VARIANT CDL 50-ARG--THR-365 DEL; CHARACTERIZATION OF VARIANTS CDLSMD SER-62 AND ARG-64; MUTAGENESIS OF ASP-276;

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.