Is B9D1 p.Arg101= (c.303A>T) pathogenic?

B9D1 p.Arg101= (c.303A>T) is classified Likely benign in B9D1 (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-27). Absent from gnomAD v4.1; Associated with Meckel syndrome.

What condition is associated with B9D1 p.Arg101= (c.303A>T)?

B9D1 p.Arg101= (c.303A>T) is associated with Meckel syndrome, Joubert syndrome (ClinVar).

How common is B9D1 p.Arg101= (c.303A>T) in the general population?

B9D1 p.Arg101= (c.303A>T) is absent from gnomAD v4.1 (gnomAD).

B9D1 p.Arg101=

c.303A>T · rs1555607998 · VCV461760

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Meckel syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP -1.7	GERP -3.7
Overall
CADD	2.449	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

Variant & gene context

Gene: B9D1
Protein: p.Arg101=
Coding: c.303A>T
MANE Select: NM_015681
dbSNP: rs1555607998
Type: single nucleotide variant
Location: chr17:19347822 (GRCh38)
Gene constraint: LOEUF 1.023 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.05
Residue 101: the c2 b9-type domain

Full B9D1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Meckel syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: Joubert syndrome

Similar variants

B9D1 p.Arg101Gln Uncertain significance ★★ same residue
B9D1 p.Arg101Gly Uncertain significance ★ ⚠ same residue
B9D1 c.341+2T>C Pathogenic/Likely pathogenic ★★ same condition
B9D1 p.Arg114Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
B9D1 p.Arg156Trp Pathogenic/Likely pathogenic ★★ same condition
B9D1 c.404+5G>C Uncertain significance ★★ same condition
B9D1 p.Ala44Val Uncertain significance ★★ ⚠ same condition
B9D1 p.Arg140Gln Uncertain significance ★★ ⚠ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/b9d1-p-arg101 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown