UniProtKB/Swiss-Prot A6NHR9: Variant p.Arg552Gln

Structural maintenance of chromosomes flexible hinge domain-containing protein 1
Gene: SMCHD1
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Variant information Variant position:

552 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 Arginine (R) to Glutamine (Q) at position 552 (R552Q, p.Arg552Gln). 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
Variant description:

In BAMS; no change in protein abundance; does not affect ATPase activity. Any additional useful information about the variant.
Other resources:

Links to websites of interest for the variant.

Variant rs886042392 [ dbSNP | Ensembl ]

Sequence information Variant position:

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

2005 The length of the canonical sequence.
Location on the sequence:

ELKLKDKNTLFTRILNGQEQ R MKIDREFALWLKDCHEKYDK 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                         ELKLKDKNTLFTRILNGQEQRMKIDREFALWLKDCHEKYDK

Mouse                         ELKLKDKNTLFTRILNGQEQRMKIDREFALWLKDCHEKHDK

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 – 2005	Structural maintenance of chromosomes flexible hinge domain-containing protein 1
Region	111 – 702	ATPase activity domain
Alternative sequence	1 – 1065	Missing. In isoform 3.
Beta strand	549 – 552

Literature citations
SMCHD1 mutations associated with a rare muscular dystrophy can also cause isolated arhinia and Bosma arhinia microphthalmia syndrome.
Shaw N.D.; Brand H.; Kupchinsky Z.A.; Bengani H.; Plummer L.; Jones T.I.; Erdin S.; Williamson K.A.; Rainger J.; Stortchevoi A.; Samocha K.; Currall B.B.; Dunican D.S.; Collins R.L.; Willer J.R.; Lek A.; Lek M.; Nassan M.; Pereira S.; Kammin T.; Lucente D.; Silva A.; Seabra C.M.; Chiang C.; An Y.; Ansari M.; Rainger J.K.; Joss S.; Smith J.C.; Lippincott M.F.; Singh S.S.; Patel N.; Jing J.W.; Law J.R.; Ferraro N.; Verloes A.; Rauch A.; Steindl K.; Zweier M.; Scheer I.; Sato D.; Okamoto N.; Jacobsen C.; Tryggestad J.; Chernausek S.; Schimmenti L.A.; Brasseur B.; Cesaretti C.; Garcia-Ortiz J.E.; Buitrago T.P.; Silva O.P.; Hoffman J.D.; Muehlbauer W.; Ruprecht K.W.; Loeys B.L.; Shino M.; Kaindl A.M.; Cho C.H.; Morton C.C.; Meehan R.R.; van Heyningen V.; Liao E.C.; Balasubramanian R.; Hall J.E.; Seminara S.B.; Macarthur D.; Moore S.A.; Yoshiura K.I.; Gusella J.F.; Marsh J.A.; Graham J.M. Jr.; Lin A.E.; Katsanis N.; Jones P.L.; Crowley W.F. Jr.; Davis E.E.; FitzPatrick D.R.; Talkowski M.E.;
Nat. Genet. 49:238-248(2017)
Cited for: INVOLVEMENT IN BAMS; VARIANTS BAMS PRO-107; LYS-129; ASN-135; CYS-135; ILE-135; ASP-136; GLU-137; HIS-139; PHE-141; VAL-171; GLY-242; ARG-345; ARG-348; LEU-400; VAL-420; GLN-473; LYS-523; SER-524 AND GLN-552; CHARACTERIZATION OF VARIANTS BAMS PRO-107; LYS-129; ASN-135; CYS-135; ILE-135; ASP-136; GLU-137; HIS-139; PHE-141; VAL-171; GLY-242; ARG-345; ARG-348; LEU-400; VAL-420; GLN-473; LYS-523; SER-524 AND GLN-552; De novo mutations in SMCHD1 cause Bosma arhinia microphthalmia syndrome and abrogate nasal development.
Gordon C.T.; Xue S.; Yigit G.; Filali H.; Chen K.; Rosin N.; Yoshiura K.I.; Oufadem M.; Beck T.J.; McGowan R.; Magee A.C.; Altmueller J.; Dion C.; Thiele H.; Gurzau A.D.; Nuernberg P.; Meschede D.; Muehlbauer W.; Okamoto N.; Varghese V.; Irving R.; Sigaudy S.; Williams D.; Ahmed S.F.; Bonnard C.; Kong M.K.; Ratbi I.; Fejjal N.; Fikri M.; Elalaoui S.C.; Reigstad H.; Bole-Feysot C.; Nitschke P.; Ragge N.; Levy N.; Tuncbilek G.; Teo A.S.; Cunningham M.L.; Sefiani A.; Kayserili H.; Murphy J.M.; Chatdokmaiprai C.; Hillmer A.M.; Wattanasirichaigoon D.; Lyonnet S.; Magdinier F.; Javed A.; Blewitt M.E.; Amiel J.; Wollnik B.; Reversade B.;
Nat. Genet. 49:249-255(2017)
Cited for: VARIANTS BAMS SER-134; ASN-135; CYS-135; GLY-136; SER-342; ARG-348; VAL-420; GLU-518 AND GLN-552; CHARACTERIZATION OF VARIANTS BAMS SER-134; CYS-135; GLY-136 AND VAL-420; CHARACTERIZATION OF VARIANTS FSHD2 CYS-353 AND MET-527; FSHD2- and BAMS-associated mutations confer opposing effects on SMCHD1 function.
Gurzau A.D.; Chen K.; Xue S.; Dai W.; Lucet I.S.; Ly T.T.N.; Reversade B.; Blewitt M.E.; Murphy J.M.;
J. Biol. Chem. 293:9841-9853(2018)
Cited for: VARIANTS FSHD2 PHE-194; ASP-263; CYS-283; CYS-353; GLU-478; MET-527 AND SER-690; VARIANTS BAMS ASN-135; GLU-137; SER-342; ARG-348; VAL-420; GLN-473; GLU-518; LYS-523 AND GLN-552; CHARACTERIZATION OF VARIANTS FSHD2 PHE-194; ASP-263; CYS-283; CYS-353; GLU-478; MET-527 AND SER-690; CHARACTERIZATION OF VARIANTS BAMS ASN-135; GLU-137; SER-342; ARG-348; VAL-420; GLN-473; GLU-518; LYS-523 AND GLN-552; FUNCTION; CATALYTIC ACTIVITY;

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.