Is SIX3 p.Pro303= (c.909G>C) pathogenic?

SIX3 p.Pro303= (c.909G>C) is classified Benign/Likely benign in SIX3 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-10-17). Rare (popmax 0.252%, sas); Associated with holoprosencephaly 2.

What condition is associated with SIX3 p.Pro303= (c.909G>C)?

SIX3 p.Pro303= (c.909G>C) is associated with holoprosencephaly 2 (ClinVar).

How common is SIX3 p.Pro303= (c.909G>C) in the general population?

SIX3 p.Pro303= (c.909G>C) is rare (popmax 0.252%, sas) (gnomAD).

SIX3 p.Pro303=

c.909G>C · rs560888073 · VCV723116

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

rare (popmax 0.252%, sas)

Conditions

holoprosencephaly 2

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 1.2	GERP -1.9, phastCons 1
Overall
CADD	11.7	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.252% South Asian · 223/88,604 alleles

Filtering AF 0.225% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.214%

Overall 0.0157% 248/1,581,820 alleles · rare

Ancestry group	Frequency	1 in
South Asiangrpmax	0.252%	397
Remaining individualsnot grpmax-eligible	0.0357%	2,801
European (non-Finnish)	0.000256%	390,598

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: SIX3
Protein: p.Pro303=
Coding: c.909G>C
MANE Select: NM_005413
dbSNP: rs560888073
Type: single nucleotide variant
Location: chr2:44944670 (GRCh38)
Gene constraint: LOEUF 0.387 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 70.38
Residue 303: the 'disordered' region

Full SIX3 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

holoprosencephaly 2 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SIX3 p.Ala72Val Uncertain significance ★★ ⚠ same condition
SIX3 p.Arg146Cys Uncertain significance ★★ ⚠ same condition
SIX3 p.Arg201His Uncertain significance ★★ ⚠ same condition
SIX3 p.Arg281Ser Uncertain significance ★★ same condition
SIX3 p.Asp205His Uncertain significance ★★ ⚠ same condition
SIX3 p.Gly103Arg Uncertain significance ★★ ⚠ same condition
SIX3 p.Gly244Cys Uncertain significance ★★ ⚠ same condition
SIX3 p.Gly317Ser 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/six3-p-pro303 (accessed [today's date]).

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