UniProtKB/SwissProt variant VAR

Variant information

Variant position:

247

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 Valine (V) to Methionine (M) at position 247 (V247M, p.Val247Met).

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:

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 OOMD9; unknown pathological significance.

Any additional useful information about the variant.

Other resources:

Links to websites of interest for the variant.

Variant rs1203102465 [ dbSNP | Ensembl ]

Sequence information

Variant position:

247

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

Protein sequence length:

432

The length of the canonical sequence.

Location on the sequence:

KLVTKMFQKIQDLIDDKDAL V FVLIDEVESLTAARNACRAG

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                         KLVTKMFQKIQDLI---DDKDALVFVLIDEVESLTAARNACRAG

                              KLVTKMFQKIQDLI---DDKDALVFVLIDEVESLTAARNAC

Mouse                         KLVTKMFQKIQDLI---DDKEALVFVLIDEVESLTAARNAC

Rat                           KLVTKMFQKIQDLI---DDKEALVFVLIDEVESLTAARNAC

Pig                           KLVTRMFQMIQDLI---DDKDALVFVLIDEVESLTAARNAC

Chicken                       KLVTKMFQKIQELI---DDKDALVFVLIDEVESLTAARSAF

Xenopus tropicalis            KLVTKMFQKIHELI---NDKEALVFVLIDEVESLTAARKAS

Zebrafish                     KLVTKMFQKIQELI---DDKDALVFVLIDEVESLTAARSAA

Caenorhabditis elegans        KLVQKMFDQIDELA---EDEKCMVFVLIDEVESLGMCRESS

Baker's yeast                 KNISIVFKDIEELLKVNEGRGIFICLLIDEVEAIASSRTNL

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 – 432	Pachytene checkpoint protein 2 homolog
Alternative sequence	171 – 406	Missing. In isoform 2.
Beta strand	245 – 251

Literature citations

Bi-allelic missense pathogenic variants in TRIP13 cause female infertility characterized by oocyte maturation arrest.
Zhang Z.; Li B.; Fu J.; Li R.; Diao F.; Li C.; Chen B.; Du J.; Zhou Z.; Mu J.; Yan Z.; Wu L.; Liu S.; Wang W.; Zhao L.; Dong J.; He L.; Liang X.; Kuang Y.; Sun X.; Sang Q.; Wang L.;
Am. J. Hum. Genet. 107:15-23(2020)
Cited for: VARIANTS OOMD9 ARG-26; GLN-173; VAL-198; MET-247 AND LYS-303; CHARACTERIZATION OF VARIANT OOMD9 ARG-26; INVOLVEMENT IN OOMD9;

UniProtKB/Swiss-Prot variant pages

UniProtKB/Swiss-Prot Q15645: Variant p.Val247Met