UniProtKB/SwissProt variant VAR

Variant information

Variant position:

339

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 Lysine (K) to Glutamine (Q) at position 339 (K339Q, p.Lys339Gln).

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 (K) 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 GADEVS; unknown pathological significance.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1555370868 [ dbSNP | Ensembl ]

Sequence information

Variant position:

339

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

Protein sequence length:

414

The length of the canonical sequence.

Location on the sequence:

THGPRVHVCAECGKAFVESS K LKRHQLVHTGEKPFQCTFEG

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                         THGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEG

Mouse                         THGPRVHVCAECGKAFVESSKLKRHQLVHTGEKPFQCTFEG

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 – 414	Transcriptional repressor protein YY1
Zinc finger	325 – 347	C2H2-type 2
Region	257 – 341	Involved in nuclear matrix association
Region	295 – 414	Binding to DNA
Region	333 – 371	Involved in repression of activated transcription
Metal binding	320 – 320	Zinc 1
Metal binding	327 – 327	Zinc 2
Metal binding	330 – 330	Zinc 2
Metal binding	343 – 343	Zinc 2
Metal binding	347 – 347	Zinc 2
Metal binding	355 – 355	Zinc 3
Helix	337 – 343

Literature citations

YY1 haploinsufficiency causes an intellectual disability syndrome featuring transcriptional and chromatin dysfunction.
Gabriele M.; Vulto-van Silfhout A.T.; Germain P.L.; Vitriolo A.; Kumar R.; Douglas E.; Haan E.; Kosaki K.; Takenouchi T.; Rauch A.; Steindl K.; Frengen E.; Misceo D.; Pedurupillay C.R.J.; Stromme P.; Rosenfeld J.A.; Shao Y.; Craigen W.J.; Schaaf C.P.; Rodriguez-Buritica D.; Farach L.; Friedman J.; Thulin P.; McLean S.D.; Nugent K.M.; Morton J.; Nicholl J.; Andrieux J.; Stray-Pedersen A.; Chambon P.; Patrier S.; Lynch S.A.; Kjaergaard S.; Toerring P.M.; Brasch-Andersen C.; Ronan A.; van Haeringen A.; Anderson P.J.; Powis Z.; Brunner H.G.; Pfundt R.; Schuurs-Hoeijmakers J.H.M.; van Bon B.W.M.; Lelieveld S.; Gilissen C.; Nillesen W.M.; Vissers L.E.L.M.; Gecz J.; Koolen D.A.; Testa G.; de Vries B.B.A.;
Am. J. Hum. Genet. 100:907-925(2017)
Cited for: VARIANTS GADEVS 179-LYS--GLN-414 DEL; TYR-320; GLN-339; 344-GLN--GLN-414 DEL; PRO-366; VAL-366; TYR-380 AND LYS-393 DEL; CHARACTERIZATION OF VARIANTS GADEVS PRO-366 AND TYR-380; FUNCTION;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot P25490: Variant p.Lys339Gln