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Table 2 Proposed causative variants in pigs

From: Evidence for and localization of proposed causative variants in cattle and pig genomes

Gene (variants)

Trait (species)

Variant type

Variant codes

Effect of alleles

Position (Sscrofa11.1)

Variant Acc

OMIA Acc

Original citation

IGF2 (g.1483817T > C)

Muscle growth

Intronic SNV

NC_010444.4:g.1483817 T > C

T has higher growth and lean meat production

2:1,483,817

  

[74]

MC4R (p.Asp298Asn)

Growth and fatness

Missense SNV

NC_010443.5:g.160773437G > A

ENSSSCP00000074588:p.Asp298Asn

A has faster growth and more fat

1:160,773,437

rs81219178

 

[82]

MSTN (p.Glu274*)

Leg weakness

Stop gain SNV

NC_010457.5:g.94623834C > A

ENSSSCP00000017001:p.Glu274*

A has leg weakness

15:94,623,834

 

OMIA 002,161–9823

 

NR6A1 (p.Leu192Pro)

Vertebrae number

Missense SNV

NC_010443.5:g.265347265A > G

ENSSSCP00000005986:p.Leu192Pro

A has higher vertebrate number

1:265,347,265

rs326780270

 

[97]

PHKG1 (g.16830320C > A)

Glycogen content and meat quality

Splice region SNV

NC_010445.4:g.16830320C > A

A has higher glycogen content

3:16,830,320

rs330928088

 

[103]

PRKAG3 (p.Arg250Gln)

Glycogen content and meat quality

Missense SNV

NC_010457.5:g.120863533C > T

ENSSSCP00000017163:p.Arg250Gln

T has high glycogen content

15:120,863,533

rs1109104772

OMIA 001,085–9823

[104]

RYR1 (p.Arg651Cys)

Malignant hypothermia

Missense SNV

NC_010448.4:g.47357966 T > C

NP_001001534.1:p.Arg651Cys

T is halothane sensitive

6:47,357,966

rs344435545

OMIA 000,621–9823

[114, 117]

SYNGR2 (p.Cys63Arg)

Porcine circovirus viral load

Missense SNV

NC_010454.4:g3797515A > C

ENSSSCP00000041695:p.Cys63Arg

A has lower viral load

12:3,797,515

  

[118]

VRTN (g.97614602A > C)

Vertebrae number

Noncoding SNV

NC_010449.5:g.97614602A > C

C has more vertebrae

7:97,614,602

rs709317845

 

[102]

(g.97615879_97615880ins)

 

Noncoding indel

NC_010449.5:g.97615879_97615880ins[AB554652.1:20312_20602]

Insertion has more vertebrae

7:97,615,880

   
  1. When there are multiple transcripts associated with a nonsynonymous variant that all give rise to the same coding consequences, we give a variant code only relative to one of them. When the gene is not available in the Ensembl gene annotation, we use NCBI annotation instead. We give variant accessions (from dbSNP, now available in Ensembl Variation and EVA), and Online Mendelian Inheritance in Animals (OMIA) accessions where available