B9D1

Chr 17AR

B9 domain containing 1

Also known as: B9, EPPB9, JBTS27, MKS9, MKSR-1, MKSR1

NCBI Gene: 27077 ENSG00000108641 UniProt: Q9UPM9 OMIM: 614144

The protein is a component of the tectonic-like complex that localizes to the transition zone of primary cilia and functions as a barrier preventing diffusion of transmembrane proteins between cilia and plasma membranes, and is required for ciliogenesis and sonic hedgehog signaling. Mutations cause Meckel syndrome 9 and Joubert syndrome 27, both severe ciliopathies affecting multiple organ systems including the brain, kidneys, and liver. Inheritance is autosomal recessive.

GeneReviews OMIM ResearchSummary from RefSeq, OMIM, UniProt

This gene encodes a B9 domain-containing protein, one of several that are involved in ciliogenesis. Alterations in expression of this gene have been found in a family with Meckel syndrome. Meckel syndrome has been associated with at least six different genes. This gene is located within the Smith-Magenis syndrome region on chromosome 17. [provided by RefSeq, Mar 2016]

GeneReviews OMIM ResearchGenerating clinical summary…

LOFmechanismARLOEUF 0.952 OMIM phenotypes

Clinical Summary— B9D1

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Gene-Disease Validity (ClinGen)

ciliopathy · ARDefinitive

Definitive — sufficient evidence for diagnostic panels

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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

8 unique Pathogenic / Likely Pathogenic· 73 VUS of 181 total submissions

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GeneReview available — B9D1

Authoritative clinical overview · Recommended first read

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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD

Tolerant — LoF & missense variants common in population

LoF Constraint?

0.95LOEUF

pLI 0.003

Z-score 1.69

OE 0.48 (0.26–0.95)

Tolerant

Typical tolerance to LoF variation

Missense Constraint?

0.10Z-score

OE missense 0.97 (0.84–1.13)

121 obs / 124.2 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.48 (0.26–0.95)

0≤0.351.4

Missense OE?0.97 (0.84–1.13)

0≤0.61.4

Synonymous OE?1.11

0≤1.21.6

LoF obs/exp: 6 / 12.4Missense obs/exp: 121 / 124.2Syn Z: -0.58

ClinVar Variant Classifications

181 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic5

Likely Pathogenic3

VUS73

Likely Benign84

Benign1

Pathogenic

Likely Pathogenic

VUS

Likely Benign

Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

Classification	LoF	Missense + Inframe	Non-coding	Synonymous	Total
Pathogenic	5	0	0	0	5
Likely Pathogenic	1	2	0	0	3
VUS	2	63	8	0	73
Likely Benign	2	9	38	35	84
Benign	0	0	1	0	1
Total	10	74	47	35	166

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

View in ClinVar →

12 pathogenic / likely-pathogenic (of 19) ClinVar copy-number / structural variants overlap B9D1 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →