UniProtKB/Swiss-Prot Q8TD31: Variant p.Arg109Trp

Coiled-coil alpha-helical rod protein 1
Gene: CCHCR1
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Variant information Variant position:

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

LB/B 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 Arginine (R) to Tryptophan (W) at position 109 (R109W, p.Arg109Trp). 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 large size and aromatic (W) 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
Polymorphism:

HCR*WWCC is associated with susceptibility to psoriasis. Psoriasis is a chronic inflammatory dermatosis that affects approximately 2% of the population. It is a multifactorial disease characterized by red, scaly skin lesions that are usually found on the scalp, elbows, and knees, and may be associated with severe arthritis. The lesions are caused by hyperproliferative keratinocytes and infiltration of inflammatory cells into the dermis and epidermis. The usual age of onset of psoriasis is between 15 and 30 years, although it can present at any age. Association of HCR with psoriasis seem to be due to linkage disequilibrium with Cw*06:02 (PubMed:11348465). HCR is unlikely to be directly involved in psoriasis development. Additional information on the polymorphism described.
Variant description:

In allele HCR*WWCC; risk factor for psoriasis. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs130076 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

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

QQAEVIVRQLQELRRLEEEV R LLRETSLQQKMRLEAQAMEL 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                         QQAEVIVRQLQELRRLEEEVRLLRETSLQQKMRLEAQAMEL

Gorilla                       QQAEVIARQLQELRRLEEEVRLLRETSLQQKMRLEAQAMEL

Chimpanzee                    QQAEVIARQLQELRRLEEEVRLLRETSLQQKMRLEAQAMEL

Mouse                         QQAELISRQLQELRRLEEEVRSLRETSLQQKMRLETQAVEL

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 – 782	Coiled-coil alpha-helical rod protein 1

Literature citations
Coding haplotype analysis supports HCR as the putative susceptibility gene for psoriasis at the MHC PSORS1 locus.
Asumalahti K.; Veal A.; Laitinen T.; Suomela S.; Allen M.; Elomaa O.; Moser M.; de Cid R.; Ripatti S.; Vorechovsky I.; Marcusson J.A.; Nakagawa H.; Lazaro C.; Estivill X.; Capon F.; Novelli G.; Burden D.B.; Tillman D.; Powis S.H.; Balendran N.; Ameen M.; Vaughan R.W.; Heath E.K.; Itkonen-Vatjus R.; Jansen C.; Karvonen J.; Karvonen S.-L.; Kivekas K.; Reunala T.; Snellman E.; Uurasmaa T.; Toftgard R.; Murakami T.; Otsuki M.; Asahina A.; Saeki H.; Barbera E.; Ferrandiz C.; Gimenez Arnau A.; Grimalt F.; Puig S.; Sanchez A.; Palacios A.; Pujol J.A.; Sanchez M.; Simal E.; Vazquez F.; Ramirez B.; Saarialho-Kere U.; Barker J.; Trembath R.; Kere J.;
Hum. Mol. Genet. 11:589-597(2002)
Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1); VARIANTS GLN-102; TRP-103; TRP-109; ARG-164; ASP-275; TRP-417; CYS-575; GLN-627; HIS-639 AND CYS-776; The DNA sequence and analysis of human chromosome 6.
Mungall A.J.; Palmer S.A.; Sims S.K.; Edwards C.A.; Ashurst J.L.; Wilming L.; Jones M.C.; Horton R.; Hunt S.E.; Scott C.E.; Gilbert J.G.R.; Clamp M.E.; Bethel G.; Milne S.; Ainscough R.; Almeida J.P.; Ambrose K.D.; Andrews T.D.; Ashwell R.I.S.; Babbage A.K.; Bagguley C.L.; Bailey J.; Banerjee R.; Barker D.J.; Barlow K.F.; Bates K.; Beare D.M.; Beasley H.; Beasley O.; Bird C.P.; Blakey S.E.; Bray-Allen S.; Brook J.; Brown A.J.; Brown J.Y.; Burford D.C.; Burrill W.; Burton J.; Carder C.; Carter N.P.; Chapman J.C.; Clark S.Y.; Clark G.; Clee C.M.; Clegg S.; Cobley V.; Collier R.E.; Collins J.E.; Colman L.K.; Corby N.R.; Coville G.J.; Culley K.M.; Dhami P.; Davies J.; Dunn M.; Earthrowl M.E.; Ellington A.E.; Evans K.A.; Faulkner L.; Francis M.D.; Frankish A.; Frankland J.; French L.; Garner P.; Garnett J.; Ghori M.J.; Gilby L.M.; Gillson C.J.; Glithero R.J.; Grafham D.V.; Grant M.; Gribble S.; Griffiths C.; Griffiths M.N.D.; Hall R.; Halls K.S.; Hammond S.; Harley J.L.; Hart E.A.; Heath P.D.; Heathcott R.; Holmes S.J.; Howden P.J.; Howe K.L.; Howell G.R.; Huckle E.; Humphray S.J.; Humphries M.D.; Hunt A.R.; Johnson C.M.; Joy A.A.; Kay M.; Keenan S.J.; Kimberley A.M.; King A.; Laird G.K.; Langford C.; Lawlor S.; Leongamornlert D.A.; Leversha M.; Lloyd C.R.; Lloyd D.M.; Loveland J.E.; Lovell J.; Martin S.; Mashreghi-Mohammadi M.; Maslen G.L.; Matthews L.; McCann O.T.; McLaren S.J.; McLay K.; McMurray A.; Moore M.J.F.; Mullikin J.C.; Niblett D.; Nickerson T.; Novik K.L.; Oliver K.; Overton-Larty E.K.; Parker A.; Patel R.; Pearce A.V.; Peck A.I.; Phillimore B.J.C.T.; Phillips S.; Plumb R.W.; Porter K.M.; Ramsey Y.; Ranby S.A.; Rice C.M.; Ross M.T.; Searle S.M.; Sehra H.K.; Sheridan E.; Skuce C.D.; Smith S.; Smith M.; Spraggon L.; Squares S.L.; Steward C.A.; Sycamore N.; Tamlyn-Hall G.; Tester J.; Theaker A.J.; Thomas D.W.; Thorpe A.; Tracey A.; Tromans A.; Tubby B.; Wall M.; Wallis J.M.; West A.P.; White S.S.; Whitehead S.L.; Whittaker H.; Wild A.; Willey D.J.; Wilmer T.E.; Wood J.M.; Wray P.W.; Wyatt J.C.; Young L.; Younger R.M.; Bentley D.R.; Coulson A.; Durbin R.M.; Hubbard T.; Sulston J.E.; Dunham I.; Rogers J.; Beck S.;
Nature 425:805-811(2003)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]; VARIANTS TRP-103; TRP-109; ARG-164; TRP-417; CYS-575 AND CYS-776; The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).
The MGC Project Team;
Genome Res. 14:2121-2127(2004)
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2); VARIANTS TRP-109; ARG-164; TRP-417; CYS-575 AND CYS-776; Association analysis using refined microsatellite markers localizes a susceptibility locus for psoriasis vulgaris within a 111kb segment telomeric to the HLA-C gene.
Oka A.; Tamiya G.; Tomizawa M.; Ota M.; Katsuyama Y.; Makino S.; Shiina T.; Yoshitome M.; Lizuka M.; Sasao Y.; Iwashita K.; Kawakubo Y.; Sugai J.; Ozawa A.; Ohkido M.; Kimura M.; Bahram S.; Inoko H.;
Hum. Mol. Genet. 8:2165-2170(1999)
Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA / MRNA] OF 20-782 (ISOFORMS 1/2); VARIANTS TRP-103; TRP-109; ARG-164; ASP-275; TRP-417; CYS-575 AND CYS-776; The HCR gene on 6p21 is unlikely to be a psoriasis susceptibility gene.
O'Brien K.P.; Holm S.J.; Nilsson S.; Carlen L.; Rosenmuller T.; Enerbaeck C.; Inerot A.; Staahle-Baeckdahl M.;
J. Invest. Dermatol. 116:750-754(2001)
Cited for: VARIANTS GLN-102; TRP-103; TRP-109; ARG-164; GLN-179; ASP-275; THR-367; TRP-417; GLN-417; CYS-575; GLN-627; VAL-733 AND CYS-776;

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.