Is SALL1 p.Pro91fs (c.269dup) pathogenic?

SALL1 p.Pro91fs (c.269dup) is classified Likely pathogenic in SALL1 (ClinVar, Single submitter, 1 submitter; last evaluated 2021-03-25). No gnomAD frequency available for this variant; Associated with Townes-Brocks syndrome 1.

What condition is associated with SALL1 p.Pro91fs (c.269dup)?

SALL1 p.Pro91fs (c.269dup) is associated with Townes-Brocks syndrome 1 (ClinVar).

How common is SALL1 p.Pro91fs (c.269dup) in the general population?

SALL1 p.Pro91fs (c.269dup) is no gnomAD frequency available for this variant (gnomAD).

SALL1 p.Pro91fs

c.269dup · rs2143452445 · VCV1048611

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Not reported

no gnomAD frequency available for this variant

Conditions

Townes-Brocks syndrome 1

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function in a LoF-intolerant gene
NMD	predicted	premature termination codon in exon 2 of 3
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP 1.7	GERP -1.9, phastCons 1
Region caveats
Repeat context	seg dup	· reads may not map uniquely · confidence, not pathogenicity

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Population frequency

dbSNP / gnomAD

No gnomAD frequency available for this variant. This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: SALL1
Protein: p.Pro91fs
Coding: c.269dup
MANE Select: NM_002968
dbSNP: rs2143452445
Type: Duplication
Location: chr16:51141952 (GRCh38)
Gene constraint: LOEUF 0.228 · pLI 1.00 · ClinGen HI 1/3 (gnomAD)
Structure: AlphaFold pLDDT 49.54
Residue 91: the 'disordered' region

Full SALL1 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

Townes-Brocks syndrome 1 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

SALL1 p.Gly161fs Pathogenic ★ same condition
SALL1 p.Ser302fs Pathogenic ★ same condition
SALL1 p.Ser385fs Pathogenic ★ same condition
SALL1 p.Val897fs Pathogenic ★ same condition
SALL1 p.Phe569_Ile570insPhe Uncertain significance ★ same condition
SALL1 p.Arg763fs Likely pathogenic same condition
SALL1 p.Val226fs Pathogenic same condition
SALL1 p.Arg1054Ter Pathogenic/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/sall1-p-pro91fs (accessed [today's date]).

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