Is GANAB p.Pro370= (c.1110C>T) pathogenic?

GANAB p.Pro370= (c.1110C>T) is classified Likely benign in GANAB (ClinVar, No assertion criteria, 1 submitter; last evaluated 2023-09-18). Very rare (popmax 8.49e-05%, nfe); Associated with GANAB-related disorder.

What condition is associated with GANAB p.Pro370= (c.1110C>T)?

GANAB p.Pro370= (c.1110C>T) is associated with GANAB-related disorder (ClinVar).

How common is GANAB p.Pro370= (c.1110C>T) in the general population?

GANAB p.Pro370= (c.1110C>T) is very rare (popmax 8.49e-05%, nfe) (gnomAD).

GANAB p.Pro370=

c.1110C>T · rs767706242 · VCV3054543

Likely benign No assertion criteria

Classification

Likely benign

ClinVar

Review

No assertion criteria ☆☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 8.49e-05%, nfe)

Conditions

GANAB-related disorder

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 0.26	GERP -4.2, phastCons 0.88
Overall
CADD	7.713	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 8.49e-05% European (non-Finnish) · 1/1,177,226 alleles

Overall 0.000657% 1/152,170 alleles · very rare

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: GANAB
Protein: p.Pro370=
Coding: c.1110C>T
MANE Select: NM_198334
dbSNP: rs767706242
Type: single nucleotide variant
Location: chr11:62631070 (GRCh38)
Gene constraint: LOEUF 0.391 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 93.43 · 2 PDB

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

Disease context

GANAB-related disorder

Similar variants

GANAB p.Pro370Ala Uncertain significance ★ ⚠ same residue
GANAB p.Arg112Ter Likely pathogenic ★★ same condition
GANAB p.Arg61Ter Pathogenic ★★ same condition
GANAB c.1150+1G>A Likely pathogenic ★ same condition
GANAB p.Arg49Ter Likely pathogenic ★ same condition
GANAB p.Ile828Met Uncertain significance ★ ⚠ same condition
GANAB p.Thr383Arg Pathogenic same condition
GANAB p.Trp501Ter Likely pathogenic 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/ganab-p-pro370 (accessed [today's date]).

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