Table 2.
Neanderthal and Denisovan nucleotide substitutions and the corresponding SIFT results on PRH2, HTN1, HTN3, AMY1A, STATH, and SMR3B gene loci.
| Chromosome Position (hg19) |
Gene Region | Modern Human | Altai Neanderthal (Variant Frequency a) |
Chagyrskaya Neanderthal (Variant Frequency a) |
Vindija Neanderthal (Variant Frequency a) |
Denisovan (Variant Frequency a) |
Codon→Amino Acid | SNP id | SNP Total Frequency (ALFA) |
SIFT Results (Score) |
|---|---|---|---|---|---|---|---|---|---|---|
| PRH2 (direct reading, chromosome 12) | ||||||||||
| 11,082,885 | Exon 2 (PRP-1) |
GTT | ATT (2%) * | ATT (12%) | ATT (4%) * | GTT (100%) | GUU→V12 AUU→I12 |
rs776898585 | A = 0% | N.S |
| 11,082,894 | Exon 2 (PRP-1) |
GTA | GTA (100%) | ATA (12%) | ATA (10%) * | GTA (100%) | GUA→V15 AUA→I15 |
n.a. | n.a. | Tolerated (0.26) |
| 11,083,305 | Exon 3 (PRP-1) |
CCA | CCA (98%) | TCA (14%) | TCA (14%) | CCA (100%) | CCA→P33 UCA→S33 |
n.a. | n.a. | Tolerated (0.07) |
| 11,083,318 | Exon 3 (PRP-1) |
GGA | GGA (100%) | GAA (14%) | GGA (100%) | GGA (100%) | GGA→G37 GAA→E37 |
n.a. | n.a. | Tolerated (0.07) |
| 11,083,323 | Exon 3 (PRP-1) |
CAA | CAA (100%) | TAA (8%) * | TAA (12%) | CAA (100%) | CAA→Q39 UAA→stop |
n.a. | n.a. | Damaging due to stop |
| 11,083,426 | Exon 3 (PRP-1) |
GGA | GGA (100%) | GGA (100%) | GAA (11%) | GGA (100%) | GGA→G73 GAA→E73 |
n.a. | n.a. | Damaging (0.02) |
| 11,083,431 | Exon 3 (PRP-1) |
CCA | CCA (100%) | TCA (13%) | TCA (8%) * | TCA (6%) * | CCA→P75 UCA→S75 |
n.a. | n.a. | Tolerated (0.23) |
| 11,083,452 | Exon 3 (PRP-1) |
GGA | GGA (100%) | AGA (6%) * | AGA (14%) | GGA (100%) | GGA→G82 AGA→R82 |
n.a. | n.a. | Damaging (0.01) |
| 11,083,455 | Exon 3 (PRP-1) |
GGC | GGC (100%) | AGC (17%) | GGC (100%) | GGC (100%) | GGC→G83 AGC→S83 |
n.a. | n.a. | N.S. |
| 11,083,488 | Exon 3 (PRP-1) |
GGA | GGA (100%) | GGA (100%) | AGA (11%) | GGA (100%) | GGA→G94 AGA→R94 |
n.a. | n.a. | Damaging (0.04) |
| 11,083,531 | Exon 3 (PRP-1) |
AGG | AGG (100%) | AGG (100%) | AAG (18%) | AGG (100%) | AGG→R108 AAG→K108 |
n.a. | n.a. | N.S. |
| 11,083,536 | Exon 3 (PRP-1) |
CAA | CAA (100%) | TAA (11%) | CAA (100%) | CAA (100%) | CAA→Q110 UAA→stop |
n.a. | n.a. | N.S. |
| 11,083,545 | Exon 3 (PRP-1) |
CCC | CCC (100%) | TCC (12%) | TCC (6%) * | CCC (100%) | CCC→P113 UCC→S113 |
rs1289206423 | T = 0% | N.S. |
| 11,083,551 | Exon 3 (PRP-1) |
CAG | CAG (97%) | CAG (100%) | TAG (13%) | CAG (100%) | CAG→Q115 UAG→stop |
n.a. | n.a. | N.S. |
| 11,083,570 | Exon 3 (PRP-1) |
GGT | GGT (100%) | GAT (18%) | GGT (100%) | GGT (100%) | GGU→G121 GAU→D121 |
n.a. | n.a. | N.S. |
| 11,083,575 | Exon 3 (PRP-1) |
CCC | CCC (96%) | TCC (8%) * | TCC (15%) | CCC (100%) | CCC→P123 UCC→S123 |
n.a. | n.a. | N.S. |
| 11,083,581 | Exon 3 (PRP-1) |
CCT | CCT (100%) | TCT (20%) | TCT (8%) * | CCT (100%) | CCU→P125 UCU→S125 |
n.a. | n.a. | N.S. |
| 11,083,582 | Exon 3 (PRP-1) |
CCT | CCT (100%) | CTT (13%) | CTT (8%) * | CCT (100%) | CCU→P125 CUU→L125 |
n.a. | n.a. | N.S. |
| 11,083,605 | Exon 3 (PRP-1) |
CCA | CCA (100%) | TCA (11%) | CCA (100%) | CCA (100%) | CCA→P133 UCA→S133 |
rs1343870622 | T = 0% | N.S. |
| 11,083,618 | Exon 3 (PRP-1) |
GGG | GGG (100%) | GAG (11%) | GGG (100%) | GGG (100%) | GGG→G137 GAG→E137 |
n.a. | n.a. | N.S. |
| 11,083,635 | Exon 3 (PRP-1) |
CCT | CCT (100%) | CCT (100%) | TCT (16%) | CCT (100%) | CCU→P143 UCU→S143 |
n.a. | n.a. | N.S. |
| 11,083,636 | Exon 3 (PRP-1) |
CCT | CCT (100%) | CCT (100%) | CTT (11%) | CCT (100%) | CCU→P143 CUU→L143 |
n.a. | n.a. | N.S. |
| 11,083,663 | Exon 3 (C-term removal) |
TCT | TCT (100%) | TCT (100%) | TTT (17%) | TCT (100%) | UCU→S152(rem) UUU→F152(rem) |
rs746351335 | n.a. | N.S. |
| HTN1 (direct reading, chromosome 4) | ||||||||||
| 70,920,165 | Exon 4 | CAT | CAT (100%) | TAT (2%) * | TAT (13%) | CAT (100%) | CAU→H15 UAU→Y15 |
n.a. | n.a. | Tolerated (0.37) |
| 70,921,215 | Exon 5 | GAA | GAA (100%) | AAA (3%) * | AAA (11%) | GAA (100%) | GAA→E16 AAA→K16 |
n.a. | n.a. | N.S |
| 70,921,234 | Exon 5 | CGA | CAA (2%) * | CAA (58%) | CAA (3%) * | CGA (100%) | CGA→R32 CAA→Q32 |
rs375127098 | A = 0.014% | N.S |
| HTN3 (direct reading, chromosome 4) | ||||||||||
| 70,896,460 | Exon 2 (Signal) |
ATG | ATG (100%) | ATA (11%) | ATG (100%) | ATG (100%) | AUG→M0(sp) AUA→I0(sp) |
n.a. | n.a. | N.S |
| 70,897,696 | Exon 3 (Signal) |
GGA | GGA (100%) | AGA (12%) | AGA (4%) * | GGA (100%) | GGA→G17(sp) AGA→R17(sp) |
rs1254624179 | n.a. | N.S |
| AMY1A (reverse reading, chromosome 1) | ||||||||||
| 104,238,248 | Exon 2 (Signal) |
ACC | ACC (100%) | ACC (100%) | ATC (15%) | ACC (100%) | UGG→W4(sp) UAG→stop |
n.a. | n.a. | Damaging due to stop |
| 104,238,189 | Exon 2 | GCT | GCT (100%) | ACT (13%) | ACT (20%) ** | GCT (100%) | CGA→R10 UGA→stop |
n.a. | n.a. | Damaging due to stop |
| 104,237,696 | Exon 3 | ACC | ACC (100%) | ACC (100%) | ATC (17%) | ACC (100%) | UGG→W59 UAG→stop |
n.a. | n.a. | Damaging due to stop |
| 104,237,685 | Exon 3 | GTT | GTT (100%) | GTT (100%) | ATT (14%) | GTT (100%) | CAA→Q63 UAA→stop |
n.a. | n.a. | Damaging due to stop |
| 104,237,626 | Exon 3 | TAC | TAC (100%) | TAC (100%) | TAT (15%) | TAC (100%) | AUG→M82 AUA→I82 |
n.a. | n.a. | Damaging (0.01) |
| 104,236,795 | Exon 4 | GCA | GCA (100%) | GCA (100%) | ACA (13%) | GCA (100%) | CGU→R92 UGU→C92 |
n.a. | n.a. | Damaging (0) |
| 104,236,666 | Exon 4 | CTA | CTA (100%) | CTA (100%) | TTA (11%) | CTA (100%) | GAU→D135 AAU→N135 |
n.a. | n.a. | Tolerated (0.08) |
| 104,236,654 | Exon 4 | CCA | CCA (100%) | TCA (5%) * | TCA (11%) | CCA (100%) | GGU→G139 AGU→S139 |
n.a. | n.a. | Tolerated (0.6) |
| 104,236,152 | Exon 5 | CAG | CAG (100%) | TAG (15%) | TAG (20%) | CAG (100%) | GUC→V157 AUC→I157 |
n.a. | n.a. | Tolerated (0.17) |
| 104,236,146 | Exon 5 | CTA | CTA (100%) | TTA (8%) * | TTA (12%) | CTA (100%) | GAU→D159 AAU→N159 |
n.a. | n.a. | Tolerated (1) |
| 104,236,139 | Exon 5 | GCA | GTA (4%) * | GTA (7%) * | GTA (12%) | GCA (100%) | CGU→R161 CAU→H161 |
n.a. | n.a. | Damaging (0.01) |
| 104,236,080 | Exon 5 | CTT | CTT (100%) | CTT (100%) | TTT (13%) | CTT (100%) | GAA→E181 AAA→K181 |
n.a. | n.a. | Tolerated (0.11) |
| 104,235,996 | Exon 5 | CGT | CGT (96%) | CGT (100%) | TGT (13%) | CGT (100%) | GCA→A209 ACA→T209 |
n.a. | n.a. | Tolerated (0.27) |
| 104,235,164 | Exon 6 | CTC | CTC (100%) | CTC (100%) | TTC (11%) | CTC (100%) | GAG→E240 AAG→K240 |
n.a. | n.a. | Damaging (0.01) |
| 104,235,148 | Exon 6 | TCA | TCA (100%) | TCA (100%) | TTA (18%) | TCA (100%) | AGU→S245 AAU→N245 |
n.a. | n.a. | Tolerated (0.52) |
| 104,235,083 | Exon 6 | GCG | ACG (3%) * | ACG (6%) * | ACG (12%) | GCG (100%) | CGC→R267 UGC→C267 |
n.a. | n.a. | Damaging (0) |
| 104,234,224 | Exon 7 | CCT | CCT (100%) | CCT (100%) | CTT (13%) | CCT (100%) | GGA→G281 GAA→E281 |
n.a. | n.a. | Damaging (0) |
| 104,234,218 | Exon 7 | CCA | CCA (100%) | CTA (13%) | CTA (15%) | CCA (100%) | GGU→G283 GAU→D283 |
n.a. | n.a. | Tolerated (0.25) |
| 104,234,129 | Exon 7 | GAA | GAA (100%) | AAA (13%) | GAA (100%) | GAA (100%) | CUU→L313 UUU→F313 |
n.a. | n.a. | Damaging (0) |
| 104,234,125 | Exon 7 | TGG | TGG (100%) | TAG (17%) | TGG (100%) | TGG (100%) | ACC→T314 AUC→I314 |
n.a. | n.a. | Damaging (0) |
| 104,233,978 | Exon 8 | GGA | GGA (100%) | AGA (13%) | AGA (11%) | GGA (100%) | CCU→P332 UCU→S332 |
n.a. | n.a. | Damaging (0.05) |
| 104,233,977 | Exon 8 | GGA | GGA (100%) | GAA (6%) * | GAA (11%) | GGA (100%) | CCU→P332 CUU→L332 |
n.a. | n.a. | Damaging (0) |
| 104,233,963 | Exon 8 | GCT | GCT (100%) | GCT (100%) | ACT (14%) | GCT (100%) | CGA→R337 UGA→stop |
rs19955486 | A = 0.08% | Damaging due to stop |
| 104,231,858 | Exon 9 | ACA | ACA (100%) | ACA (100%) | ATA (11%) | ACA (100%) | UGU→C378 UAU→Y378 |
n.a. | n.a. | Damaging (0) |
| 104,231,680 | Exon 10 | CAC | CAC (100%) | TAC (4%) * | TAC (20%) | CAC (100%) | GUG→V401 AUG→M401 |
n.a. | n.a. | Damaging (0) |
| 104,231,643 | Exon 10 | CCC | CCC (100%) | CTC (5%) * | CTC (11%) | CCC (100%) | GGG→G413 GAG→E413 |
n.a. | n.a. | Damaging (0.02) |
| 104,231,622 | Exon 10 | CCC | CCC (100%) | CCC (100%) | CTC (13%) | CCC (100%) | GGG→G420 GAG→E420 |
n.a. | n.a. | Tolerated (0.08) |
| 104,230,237 | Exon 11 | TGA | TGA (100%) | TGA (100%) | TAA (13%) | TGA (100%) | ACU→T442 AUU→I442 |
n.a. | n.a. | Damaging (0) |
| 104,230,129 | Exon 11 | AGA | AGA (100%) | AGA (100%) | AAA (13%) | AGA (100%) | UCU→S478 UUU→F478 |
n.a. | n.a. | Tolerated (0.62) |
| STATH (direct reading, chromosome 4) | ||||||||||
| 70,866,583 | Exon 5 | GGG | GGG (100%) | AGG (13%) | AGG (3%) * | GGG (100%) | GGG→G17 AGG→R17 |
n.a. | n.a. | N.A. |
| 70,866,616 | Exon 5 | CCA | CCA (98%) | CCA (100%) | TCA (11%) | TCA (3%) * | CCA→P28 UCA→S28 |
n.a. | n.a. | N.A. |
| 70,866,626 | Exon 5 | CCA | CCA (100%) | CTA (15%) | CCA (100%) | CCA (96%) | CCA→P31 CUA→L31 |
n.a. | n.a. | N.A. |
| 70,866,628 | Exon 5 | CAA | CAA (100%) | TAA (15%) | CAA (100%) | CAA (100%) | CAA→Q32 UAA→stop |
n.a. | n.a. | Damaging due to stop |
| SMR3B (direct reading, chromosome 4) | ||||||||||
| 71,255,405 | Exon 3 | AGG | AGG (100%) | AGG (100%) | AAG (12%) | AGG (100%) | AGG→R5 AAG→K5 |
rs777831757 | A = 0% | NS |
| 71,255,444 | Exon 3 | CCT | CCT (100%) | CTT (12%) | CTT (3%) * | CCT (100%) | CCU→P18 CUU→L18 |
n.a. | n.a. | NS |
| 71,255,495 | Exon 3 | GGG | GGG (100%) | GGG (94%) | GAG (17%) | GGG (100%) | GGG→G35 GAG→E35 |
n.a. | n.a. | NS |
a: Frequency of the substitution (highlighted bases) in the ancient hominin species, as reported in IGV considering the depth (coverage) of the reads displayed at the corresponding locus; * frequency ≤ 10% and ** counts < 10; n.a.: not available; NS: not scored.