Table 2 Rare genomic SNVs, INDELs and CNVs identified in the Chromosome 9 (chr9: 12,400,417–113,467,798) linked region.
Gene | rs | bp | Ref | Obs | Protein impact | 1000G | ExAC | gnomAD | Varsome | Subjects | |
|---|---|---|---|---|---|---|---|---|---|---|---|
Rare SNPs coding regions | |||||||||||
ZNF618 | rs762985449 | 116,811,096 | G | A | R505H | NA | 0.0000 | 0.0000 | VUS | 1–3, 1–6 | |
rs770522574 | 116,811,450 | C | T | T623M | NA | 0.0000 | 0.0000 | VUS | 1–18 | ||
TNC | rs61729478 | 117,848,368 | C | T | V548M | 0.0064 | 0.0099 | 0.0091 | Likely benign | 3–31 | |
CDK5RAP2 | rs41296081 | 123,239,643 | A | G | L571P | 0.0032 | 0.0087 | 0.0084 | Benign | 1–6, 3–11, 3–12 | |
C5 | rs139479771 | 123,762,323 | C | A | A857S | 0.0022 | 0.0000 | 0.0061 | Likely benign | 3–13, 3–30 | |
rs34552775 | 123,785,738 | G | T | L360M | 0.0010 | 0.0052 | 0.0053 | Benign | 1–6, 3–11, 3–12 | ||
GSN | rs116185403 | 124,083,642 | C | T | A481C | 0.0016 | 0.0016 | 0.0030 | Likely benign | 1–2, 1–3, 1–6, 1–18, 1–21, 1–25 | |
Rare SNPs non-coding regions | |||||||||||
Narrow | MUSK | rs149296909 | 113,479,998 | T | C | Intronic | 0.0058 | NA | 0.0030 | Likely benign | 3–11, 3–12, 3–30, 3–31 |
rs368429456 | 113,481,468 | G | T | Intronic | 0.0058 | NA | 0.0028 | Likely benign | 3–11, 3–12, 3–30, 3–31 | ||
rs183670470 | 113,515,498 | G | A | Intronic | 0.0012 | NA | 0.0018 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs79303192 | 113,525,126 | G | A | Intronic | 0.0014 | NA | 0.0020 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs149348343 | 113,548,471 | G | A | Intronic | 0.0010 | NA | 0.0019 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
LPAR1 | rs146624388 | 113,642,528 | G | T | Intronic | 0.0010 | NA | 0.0012 | VUS | 3–11, 3–12, 3–30, 3–31 | |
rs147609101 | 113,681,896 | G | A | Intronic | 0.0070 | NA | 0.0065 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs72748167 | 113,684,505 | G | A | Intronic | 0.0038 | NA | 0.0071 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs375075858 | 113,727,420 | T | C | Intronic | 0.0008 | NA | 0.0014 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs187952001 | 113,727,561 | G | T | Intronic | 0.0008 | NA | 0.0015 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs72750194 | 113,745,730 | A | C | Intronic | 0.0030 | NA | 0.0074 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
NA | rs369362681 | 113,878,682 | A | G | Intergenic | NA | NA | 0.0049 | VUS | 3–11, 3–12, 3–30, 3–31 | |
C9orf84 | NA | 114,553,050 | A | T | Intronic | Not reported | VUS | 3–11, 3–12, 3–30, 3–31 | |||
UGCG | rs182375662 | 114,669,858 | G | A | Intronic | 0.0014 | NA | 0.0014 | VUS | 3–11, 3–12, 3–30, 3–31 | |
NA | rs117263726 | 114,768,926 | A | G | Intergenic | 0.0020 | NA | 0.0020 | VUS | 3–11, 3–12, 3–30, 3–31 | |
PTBP3 | rs147275436 | 115,011,769 | G | A | Intronic | NA | NA | 0.0001 | VUS | 3–11, 3–12, 3–30, 3–31 | |
KIAA1958 | rs564854273 | 115,257,089 | T | C | Intronic | 0.0002 | NA | 0.0001 | VUS | 3–11, 3–12, 3–30, 3–31 | |
rs556349267 | 115,259,293 | T | C | Intronic | 0.0002 | NA | 0.0001 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs183650808 | 115,300,353 | G | A | Intronic | 0.0018 | NA | 0.0004 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
rs144366338 | 115,303,659 | T | C | Intronic | 0.0014 | NA | 0.0014 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
NA | rs574327747 | 115,443,505 | T | A | Intergenic | 0.0020 | NA | 0.0005 | VUS | 3–11, 3–12, 3–30, 3–31 | |
FKBP15 | rs141811808 | 115,960,045 | A | G | Intronic | 0.0040 | NA | 0.0023 | Likely benign | 3–11, 3–12, 3–30, 3–31 | |
NA | 115,978,421 | A | G | Intronic | NA | NA | 0.0017 | VUS | 3–11, 3–12, 3–30, 3–31 | ||
NA | rs151159543 | 116,144,471 | T | C | Intergenic | 0.0058 | NA | 0.0096 | VUS | 3–11, 3–12, 3–30, 3–31 | |
ZNF618 | rs530450539 | 116,794,577 | A | C | Intronic | 0.0008 | NA | 0.0020 | VUS | 3–11, 3–12, 3–30, 3–31 | |
DELEC1 | rs537057975 | 118,135,400 | A | G | Intronic | 0.0002 | NA | 0.0000 | VUS | 3–11, 3–12, 3–30, 3–31 | |
Wide | NA | rs145813581 | 116,883,714 | A | G | Intergenic | 0.0036 | NA | 0.0077 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 |
COL27A1 | rs187396762 | 116,999,043 | G | T | Intronic | 0.0020 | NA | 0.0061 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
rs117732536 | 117,017,282 | G | A | Intronic | 0.0046 | NA | 0.0085 | Likely benign | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
WHRN | NA | 117,180,316 | A | G | Intronic | Not reported | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |||
NA | rs72754560 | 117,491,583 | A | G | Intergenic | 0.0048 | NA | 0.0061 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs146845932 | 117,503,577 | C | T | Intergenic | 0.0056 | NA | 0.0062 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs56000964 | 117,523,825 | C | T | Intergenic | 0.0048 | NA | 0.0061 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs56008628 | 117,531,509 | C | T | Intergenic | 0.0034 | NA | 0.0050 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | NA | 117,754,194 | C | A | Intergenic | NA | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
TNC | rs944511 | 117,843,831 | G | T | Intronic | 0.0020 | NA | 0.0030 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
rs2482079 | 117,868,293 | T | C | Intronic | 0.0022 | NA | 0.0030 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
NA | 117,878,534 | G | A | Intronic | NA | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
DELEC1 | rs2992149 | 117,926,298 | G | A | Intronic | 0.0040 | NA | 0.0035 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | 118,116,520 | A | G | Intronic | NA | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs537057975 | 118,135,400 | A | G | Intronic | 0.0002 | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs545046369 | 118,142,492 | G | A | Intronic | 0.0002 | NA | 0.0001 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
NA | rs571168692 | 118,405,585 | C | T | Intergenic | 0.0002 | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | NA | 118,522,840 | G | A | Intergenic | NA | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | NA | 118,550,150 | C | T | Intergenic | NA | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs146826488 | 118,613,045 | A | G | Intergenic | 0.0094 | NA | 0.0040 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs147559462 | 118,858,914 | A | G | Intergenic | 0.0032 | NA | 0.0040 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
PAPPA | NA | 118,976,797 | C | A | Intronic | Not reported | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |||
NA | 119,022,095 | T | C | Intronic | Not reported | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||||
NA | 119,024,387 | G | A | Intronic | Not reported | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||||
rs181003102 | 119,063,932 | A | T | Intronic | 0.0010 | NA | 0.0036 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
ASTN2 | rs186435615 | 119,198,874 | G | A | Intronic | 0.0008 | NA | 0.0033 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
rs139814838 | 119,219,573 | A | G | Intronic | 0.0028 | NA | 0.0080 | Likely benign | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
NA | 119,270,176 | T | C | Intronic | Not reported | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||||
rs116995922 | 119,318,987 | C | T | Intronic | 0.0028 | NA | 0.0077 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs117517893 | 119,325,920 | C | T | Intronic | 0.0030 | NA | 0.0083 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs188489544 | 119,340,790 | T | C | Intronic | 0.0028 | NA | 0.0077 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs150169463 | 119,371,830 | T | C | Intronic | 0.0028 | NA | 0.0078 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
NA | 119,437,954 | G | A | Intronic | Not reported | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||||
rs117579154 | 119,484,619 | A | G | Intronic | 0.0026 | NA | 0.0088 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs534176897 | 119,684,901 | C | T | Intronic | NA | NA | 0.0000 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs186219478 | 119,816,588 | T | C | Intronic | 0.0016 | NA | 0.0048 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs117473036 | 119,961,964 | T | C | Intronic | 0.0020 | NA | 0.0048 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs146129313 | 119,966,382 | G | C | Intronic | 0.0016 | NA | 0.0040 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs149483580 | 120,026,166 | C | T | Intronic | 0.0016 | NA | 0.0052 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
rs191594200 | 120,105,136 | G | A | Intronic | 0.0004 | NA | 0.0011 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | ||
NA | rs191347609 | 121,565,707 | G | A | Intergenic | 0.0004 | NA | 0.0029 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs117766598 | 121,868,452 | T | C | Intergenic | 0.0032 | NA | 0.0080 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs181505483 | 122,175,429 | A | G | Intergenic | 0.0022 | NA | 0.0018 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs191352043 | 122,192,299 | T | C | Intergenic | 0.0020 | NA | 0.0015 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs4837653 | 122,292,842 | A | G | Intergenic | 0.0006 | NA | 0.0008 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs186447793 | 122,530,344 | G | A | Intergenic | 0.0022 | NA | 0.0011 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs150164433 | 122,542,663 | A | G | Intergenic | 0.0030 | NA | 0.0091 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs191966830 | 122,555,982 | T | G | Intergenic | 0.0054 | NA | 0.0032 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
NA | rs145380362 | 122,611,729 | T | C | Intergenic | 0.0062 | NA | 0.0045 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
Rare INDELS non-coding regions | |||||||||||
DELEC1 | NA | 118,113,219 | AAGG | A | Intronic | NA | NA | 0.0001 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
LINC00474 | NA | 118,667,077 | ATG | A | Intronic | NA | NA | 0.0001 | VUS | 3–11, 3–12, 3–13, 3–30, 3–31 | |
HSDL2 | NA | 115,184,679 | TCCTGACATAAG | T | Intronic | NA | NA | NA | VUS | 3–9, 3–10, 3–11, 3–12, 3–30, 3–31, 3–33 | |
ZNF618 | NA | 116,646,033 | A | ATAT | Intronic | NA | NA | NA | VUS | 3–8, 3–30, 3–34 | |
DELEC1 | NA | 118,111,076 | TCA | T | Intronic | NA | NA | NA | VUS | 3–30 | |
PAPPA | rs748913197 | 119,154,431 | G | GCACA | Intronic | NA | NA | NA | VUS | 1–24, 1–25, 1–26, 1–27 | |
ASTN2 | NA | 120,127,502 | GAA | G | Intronic | NA | NA | NA | VUS | 1–25 | |
Gene | Start | End | CNV | Size (bp) | Protein impact | Decipher | |||||
|---|---|---|---|---|---|---|---|---|---|---|---|
CNVs coding regions | |||||||||||
DELEC1 | 118,067,401 | 118,070,500 | DEL | 3099 | Gene | Not reported | 1–18, 1–19 | ||||
CNVs non-coding regions | |||||||||||
NA | 113,669,166 | 113,669,260 | DEL | 94 | inton_variant | Not reported | 1–18, 1–19, 3–13 | ||||
NA | 114,597,069 | 114,597,147 | DEL | 78 | Intergenic | Not reported | 1–2, 1–5 | ||||
NA | 116,463,148 | 116,463,353 | DEL | 205 | Intergenic | Not reported | 3–29, 3–31, 3–33 | ||||
NA | 120,596,847 | 120,597,027 | DEL | 180 | Intergenic | Not reported | 1–18, 1–19, 3–8, 3–30 | ||||
