Table 3 Homozygous Finnish enriched variants observed ≥2 times across NFID and the Southern and Northern Finnish NDD cases and not observed in any controls as homozygous

From: Contribution of rare and common variants to intellectual disability in a sub-isolate of Northern Finland

Variant

Gene

Previous evidence

GnomAD Finnish AF

GnomAD pop. Max AF

NFID AF

RAFT meta p

NFID case homs

NFID RAFT p

Population NDD case homs

Population NDD RAFT p

12:94243956 G:A (mis)

CRADD

AR Lissencephaly, ID25

6.01E−3

9.15E−4

7.83E−3

5.01E−8 a

3

1.86E−6

1

9.30E−3

7:81374424 G:C (mis)

HGF

AR hearing loss (OMIM)

1.12E−3

5.48E−4

2.52E−3

1.34E−5 a

1

3.20E−3

1

2.54E−3

12:15784582 T:C (mis)

EPS8

AR deafness (OMIM) Cognition defects in mice51

9.03E−3

1.30E−3

6.89E−3

1.28E−4

2

1.28E−4

0

NA

1:220236134 C:T (mis)

BPNT1

-

1.07E−2

4.83E−3

6.89E−3

1.34E−4

2

1.34E−4

0

NA

7:1520077 T:C (mis)

INTS1

AR ID26

1.30E−2

3.05E−3

1.71E−2

1.95E−4

3

1.95E−4

0

NA

2:95753239 A:G (mis)

MRPS5

-

9.87E−3

4.56E−3

8.29E−3

2.88E−4

2

2.88E−4

0

NA

10:123844296 C:A (mis)

TACC2

-

1.32E−2

1.10E−3

1.14E−2

1.05E−3

2

1.05E−3

0

NA

1:155028692 C:T (mis)

ADAM15

-

8.69E−3

2.37E−3

1.18E−2

2.11E−3

1

4.84E−2

1

3.58E−2

18:14542688 G:A (mis)

POTEC

-

1.86E−2

6.26E−3

1.98E−2

2.11E−3

2

1.01E−2

1

1.65E−1

21:19651329 G:C (mis)

TMPRSS15

Enterokinase deficiency (OMIM)

1.73E−2

6.31E−3

1.93E−2

2.66E−3

1

1.42E−1

2

9.85E−3

15:60789800 T:C (mis)

RORA

AD ID52

1.02E−2

9.14E−4

1.59E−2

4.03E−3

1

9.35E−2

1

3.38E−2

11:6023849 C:T (mis)

OR56A4

-

1.69E−2

1.82E−3

1.61E−2

4.45E−3

2

4.45E−3

0

NA

11:3681309 G:A (mis)

ART1

-

1.64E−2

3.68E−3

1.53E−2

5.67E−3

1

8.43E−2

1

5.76E−2

19:56424477 TC:T (frameshift)

NLRP13

-

1.65E−2

1.28E−3

1.40E−2

6.07E−3

1

7.44E−2

1

8.54E−2

8:17612739 G:C (mis)

MTUS1

-

1.46E−2

2.01E−3

1.54E−2

6.74E−3

1

9.22E−2

1

7.45E−2

1:183520048 A:T (mis)

SMG7

NMD-components linked to ID53

2.49E−2

1.10E−3

2.62E−2

3.85E−2

1

2.85E−1

1

1.58E−1

X:23410887 C:T (mis)

PTCHD1

x-linked ID/AUTISM54

2.43E−4

2.51E−5

2.27E−4

NA

1b

NA

1b

NAb

  1. AR autosomal recessive, AD autosomal dominant, ID intellectual disability, AF allele frequency, mis missense
  2. aSignificant after multiple testing correction
  3. bRAFT statistic not valid for X-chromosome. Both carriers are hemizygote males
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