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. Author manuscript; available in PMC: 2021 Jun 3.
Published in final edited form as: Hum Mutat. 2020 Jan 23;41(3):543–580. doi: 10.1002/humu.23968

Table 8:

HPS6 Pathogenic Gene Variants Associated with Hermansky-Pudlak Syndrome Type 6 (HPS-6)

No mRNA NM_024747.5 Amino Acid NP_079023.2 Exon/Intron 1 Variant Type 2 Ethnic Background 3 References and Footnotes
1 c.62_63insCGGCG p.Leu22Glyfs*33 Exon 1 Indel - (Lasseaux et al., 2018) 4
2 c.60_64dupGCGGC p.Leu22Argfs*33 Exon 1 Indel Chinese, Japanese, Portuguese (Bastida et al., 2019; Okamura et al., 2018; Wei et al., 2016; Wei et al., 2019) 4
3 c.87_108dup22 p.Ser37Leufs*146 Exon 1 Indel Czech, Eastern/Northern European, German, Polish (Radke et al., 2013; Summers & Schimmenti, 2014) 5
4 c.141_143delinsG p.Pro49Trpfs*126 Exon 1 Indel - (Lasseaux et al., 2018) 4
5 c.155delT p.Val52Glufs*6 Exon 1 Frameshift Chinese (Wei et al., 2016) 4
6 c.206_210dupGGGCC p.Trp71Glyfs*158 Exon 1 Indel Chinese (Wei et al., 2019) 4
7 c.223C>T p.Gln75* Exon 1 Nonsense Italian (Huizing et al., 2009)
8 c.233C>G p.Pro78Arg 6 Exon 1 Missense Japanese (Okamura et al., 2019) 4
9 c.238dupG p.Asp80Glyfs*96 Exon 1 Frameshift Dutch, German (Huizing et al., 2009)
10 c.275T>A p.Leu92Gln 7 Exon 1 Missense - (Lasseaux et al., 2018) 4,7
11 c.288G>A p.Trp96* Exon 1 Nonsense Arabic (Khan et al., 2016) 4
12 c.337C>T p.Arg113Trp Exon 1 Missense - (Lasseaux et al., 2018) 4
13 c.383T>C p.Val128Ala Exon 1 Missense Caucasian (Han et al., 2018) 4
14 c.448_505dup58 p.Glu169Glyfs*26 Exon 1 Indel Caucasian novel 4,8,9
15 c.455C>G p.Ser152* Exon 1 Nonsense - (Lasseaux et al., 2018) 4
16 c.503_504delTG p.Leu168Argfs*7 Exon 1 Indel Chinese (Wei et al., 2019) 4
17 c.779G>A p.Gly260Glu Exon 1 Missense Punjabi Afghan (Hull et al., 2016) 4
18 c.815C>T p.Thr272Ile Exon 1 Missense Dutch, German (Huizing et al., 2009)
19 c.823C>T p.Pro275Ser Exon 1 Missense Pakistani (Yousaf et al., 2016) 4
20 c.877C>T p.Glu293* Exon 1 Nonsense - (Shamseldin et al., 2017) 4
21 c.895C>T p.Arg299Trp Exon 1 Missense Chinese (Wei et al., 2016) 4
22 c.896G>C p.Arg299Pro Exon 1 Missense - (Lasseaux et al., 2018) 4
23 c.905G>A p.Gly302Asp Exon 1 Missense - (Lasseaux et al., 2018) 4
24 c.902dupT p.Thr303Hisfs*64 Exon 1 Frameshift Russian-Palestinian (Hull et al., 2016) 4
25 c.913C>T p.Gln305* Exon 1 Nonsense English, German, Scottish (Huizing et al., 2009)
26 c.1065dupG 10 p.Leu356Alafs*11 Exon 1 Frameshift Israeli Bedouin (Schreyer-Shafir et al., 2006) 10
27 c.1083dupC p.Gly362Argfs*5 Exon 1 Frameshift Russian-Palestinian (Hull et al., 2016) 4
28 c.1114 C>T p.Arg372* Exon 1 Nonsense Irish, Native American (Cherokee), Scottish (O'Brien et al., 2016)
29 c.1234C>T p.Gln412* Exon 1 Nonsense Italian (Huizing et al., 2009)
30 c.1235_1239dupAGCGG p.Arg414Serfs*15 Exon 1 Indel Chinese (Wei et al., 2019) 4
31 c.1372delG p.Glu458Serfs*8 Exon 1 Frameshift Chinese (Wei et al., 2016) 4
32 c.1387C>T p.Arg463* Exon 1 Nonsense - (Lasseaux et al., 2018) 4
33 c.1513C>T p.Gln505* Exon 1 Nonsense Chinese (Wei et al., 2016; Wei et al., 2019) 4
34 c.1644delA p.Gly550Glufs*2 Exon 1 Frameshift Arabic (Khan et al., 2016) 4
35 c.1711_1712insAG p.Cys571* Exon 1 Indel Czech, Eastern/Northern European, German, Polish (Radke et al., 2013; Summers & Schimmenti, 2014) 5
36 c.1714_1717delCTGT p.Leu572Alafs*40 Exon 1 Indel Belgian (Lasseaux et al., 2018; Zhang et al., 2003) 4
37 c.1819C>T p.Arg607* Exon 1 Nonsense Chinese (Lasseaux et al., 2018; Wei et al., 2019) 4
38 c.1865_1866delTG p.Leu622Argfs*12 Exon 1 Indel German, Irish (Huizing et al., 2009)
39 c.1898delC p.Pro633Leufs*76 Exon 1 Frameshift Japanese (Miyamichi et al., 2016) 4
40 c.1919_1920delTC p.Val640Glyfs*29 Exon 1 Indel German-Caucasian (Andres et al., 2017) 4
41 c.2038C>T p.Gln680* Exon 1 Nonsense Japanese (Miyamichi et al., 2016; Okamura et al., 2018; Okamura et al., 2019) 4, 11
42 c.2189dupC p.Leu731Serfs*28 Exon 1 Frameshift Caucasian novel 4,8,9
43 c.2207T>C p.Leu736Pro Exon 1 Missense - (Lasseaux et al., 2018) 4
44 del19,972-bp 12 - Exon 1 Indel English, German, Scottish (Huizing et al., 2009)
45 del exon 1 12 - Exon 1 Indel - (Lasseaux et al., 2018) 4
1

The HPS6 gene consists of 1 exon.

2

When deletion/insertion is 1 nucleotide it is named Frameshift, when larger it is named Indel.

3

Extracted from literature reference. ‘-‘ = unreported.

4

At least one of the reported individuals with this variant was identified by next generation sequencing.

5

The subject described in these references was also seen at NIH and is of Eastern/Northern European (Czech, German, Polish) descent. This subject is compound heterozygous for c.87_108dup22-bp and c.1711_1712insAG.

6

Gray highlight: missense variant. See text and Supplemental Tables for pathogenicity description.

7

This variant is listed as a variant of uncertain significance with a high MAF in the ClinVar database (https://www.ncbi.nlm.nih.gov/clinvar/).

8

novel = previously unreported variant and/or ethnicity, detected in the NIH HPS cohort.

9

This HPS6 variant was identified by exome sequencing in one unreported subject of Caucasian descent in the NIH HPS cohort. This subject is compound heterozygous for c.448_505dup58-bp and c.2189dupC.

10

This frameshift variant was previously described as c.1066_1067insG (p.Leu356Argfs*11) (Schreyer-Shafir et al., 2006).

11

This HPS6 variant c.2038C>T (p.Gln680*) appears to be a Japanese variant, as it occurs in 5 Japanese subjects and is not reported in dbSNP/ExAc databases.

12

The nomenclature of these HPS6 variants are included in this Table as reported, see reference for each specific variant for more details.