Is SIX3 p.Pro277= (c.831G>A) pathogenic?

SIX3 p.Pro277= (c.831G>A) is classified Likely benign in SIX3 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-01). Ultra-rare (popmax 0.0518%, nfe); Associated with holoprosencephaly 2.

What condition is associated with SIX3 p.Pro277= (c.831G>A)?

SIX3 p.Pro277= (c.831G>A) is associated with holoprosencephaly 2 (ClinVar).

How common is SIX3 p.Pro277= (c.831G>A) in the general population?

SIX3 p.Pro277= (c.831G>A) is ultra-rare (popmax 0.0518%, nfe) (gnomAD).

SIX3 p.Pro277=

c.831G>A · rs370941478 · VCV259763

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0518%, nfe)

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 -0.97	GERP -1.9
Overall
CADD	6.894	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0518% European (non-Finnish) · 606/1,169,206 alleles

Filtering AF 0.0484% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0471%

Overall 0.0405% 640/1,578,362 alleles · ultra-rare

Ancestry group	Frequency	1 in
European (non-Finnish)grpmax	0.0518%	1,929
Remaining individualsnot grpmax-eligible	0.0342%	2,922
Admixed American	0.0137%	7,298
African / African-American	0.00674%	14,845

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.Pro277=
Coding: c.831G>A
MANE Select: NM_005413
dbSNP: rs370941478
Type: single nucleotide variant
Location: chr2:44944592 (GRCh38)
Gene constraint: LOEUF 0.387 · pLI 0.99 · ClinGen HI 3/3 (gnomAD)
Structure: AlphaFold pLDDT 70.38
Residue 277: 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.Pro277Gln Benign ★ same residue
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

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-pro277 (accessed [today's date]).

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