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UniProtKB/Swiss-Prot Q12873: Variant p.Leu1236Pro

Chromodomain-helicase-DNA-binding protein 3
Gene: CHD3
Variant information

Variant position:  1236
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 Leucine (L) to Proline (P) at position 1236 (L1236P, p.Leu1236Pro).
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:  Similar physico-chemical property. Both residues are medium size and hydrophobic.
The physico-chemical property of the reference and variant residues and the change implicated.

BLOSUM score:  -3
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 SNIBCPS.
Any additional useful information about the variant.

Other resources:  
Links to websites of interest for the variant.



Sequence information

Variant position:  1236
The position of the amino-acid change on the UniProtKB canonical protein sequence.

Protein sequence length:  2000
The length of the canonical sequence.

Location on the sequence:   KAGSMSKQELDDILKFGTEE  L FKDENEGENKEEDSSVIHYD
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                         KAG-SMSKQELDDILKFGTEELFKDEN------EGE---NKEEDSSVIHYD

Caenorhabditis elegans        KDGKSMSKTELDDVLRWGTEELFKEEEAPVEGADGEGTSSK

Drosophila                    MTT-NFSKDELEDILRFGTEDLFK---------DGK-----

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 – 2000 Chromodomain-helicase-DNA-binding protein 3
Modified residue 1219 – 1219 Phosphoserine
Cross 1222 – 1222 Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Cross 1238 – 1238 Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)
Cross 1246 – 1246 Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO2)


Literature citations

CHD3 helicase domain mutations cause a neurodevelopmental syndrome with macrocephaly and impaired speech and language.
Snijders Blok L.; Rousseau J.; Twist J.; Ehresmann S.; Takaku M.; Venselaar H.; Rodan L.H.; Nowak C.B.; Douglas J.; Swoboda K.J.; Steeves M.A.; Sahai I.; Stumpel C.T.R.M.; Stegmann A.P.A.; Wheeler P.; Willing M.; Fiala E.; Kochhar A.; Gibson W.T.; Cohen A.S.A.; Agbahovbe R.; Innes A.M.; Au P.Y.B.; Rankin J.; Anderson I.J.; Skinner S.A.; Louie R.J.; Warren H.E.; Afenjar A.; Keren B.; Nava C.; Buratti J.; Isapof A.; Rodriguez D.; Lewandowski R.; Propst J.; van Essen T.; Choi M.; Lee S.; Chae J.H.; Price S.; Schnur R.E.; Douglas G.; Wentzensen I.M.; Zweier C.; Reis A.; Bialer M.G.; Moore C.; Koopmans M.; Brilstra E.H.; Monroe G.R.; van Gassen K.L.I.; van Binsbergen E.; Newbury-Ecob R.; Bownass L.; Bader I.; Mayr J.A.; Wortmann S.B.; Jakielski K.J.; Strand E.A.; Kloth K.; Bierhals T.; Roberts J.D.; Petrovich R.M.; Machida S.; Kurumizaka H.; Lelieveld S.; Pfundt R.; Jansen S.; Deriziotis P.; Faive L.; Thevenon J.; Assoum M.; Shriberg L.; Kleefstra T.; Brunner H.G.; Wade P.A.; Fisher S.E.; Campeau P.M.;
Nat. Commun. 9:4619-4619(2018)
Cited for: FUNCTION; CATALYTIC ACTIVITY; INVOLVEMENT IN SNIBCPS; VARIANTS SNIBCPS 457-GLU--ASP-2000 DEL; ARG-886; PHE-915; LYS-921; GLU-961; GLN-985; TRP-985; GLY-1109 DEL; HIS-1120; PRO-1121; ILE-1136; ARG-1158; LYS-1159; ARG-1161; TRP-1169; ARG-1171; GLN-1172; PRO-1187; PRO-1236; GLN-1342 AND LEU-1881; CHARACTERIZATION OF VARIANTS SNIBCPS PHE-915; PRO-1121; ARG-1158; LYS-1159; GLN-1172 AND PRO-1187;

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.