SEC16B

Chr 1

SEC16 homolog B, endoplasmic reticulum export factor

Also known as: LZTR2, PGPR-p117, RGPR, RGPR-p117, SEC16S

NCBI Gene: 89866 ENSG00000120341 UniProt: Q96JE7 OMIM: 612855

SEC16B is a mammalian homolog of S. cerevisiae Sec16 that is required for organization of transitional endoplasmic reticulum (ER) sites and protein export (Bhattacharyya and Glick, 2007 [PubMed 17192411]).[supplied by OMIM, Jun 2009]

OMIM Research

OMIM ResearchGenerating clinical summary…

LOEUF 0.96

Clinical Summary— SEC16B

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Population Constraint (gnomAD)

Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.

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ClinVar Variants

163 VUS of 216 total submissions

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.96LOEUF

pLI 0.000

Z-score 1.80

OE 0.75 (0.60–0.96)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.35Z-score

OE missense 0.96 (0.89–1.03)

546 obs / 569.6 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.75 (0.60–0.96)

0≤0.351.4

Missense OE?0.96 (0.89–1.03)

0≤0.61.4

Synonymous OE?0.90

0≤1.21.6

LoF obs/exp: 47 / 62.3Missense obs/exp: 546 / 569.6Syn Z: 1.21

ClinVar Variant Classifications

216 submitted variants in ClinVar

ClinVar

Classification Summary

VUS163

Likely Benign21

Benign5

Conflicting1

163

VUS

Likely Benign

Benign

Conflicting

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	0	0	0	0	0
Likely Pathogenic	0	0	0	0	0
VUS	0	163	0	0	163
Likely Benign	0	19	0	2	21
Benign	0	5	0	0	5
Conflicting	—				1
Total	0	187	0	2	190

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

23 pathogenic / likely-pathogenic (of 25) ClinVar copy-number / structural variants overlap SEC16B — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →