Is LFNG p.Ser241= (c.723C>T) pathogenic?

LFNG p.Ser241= (c.723C>T) is classified Likely benign in LFNG (ClinVar, Single submitter, 2 submitters; last evaluated 2025-12-22). Ultra-rare (popmax 0.0919%, afr); Associated with spondylocostal dysostosis 3, autosomal recessive.

What condition is associated with LFNG p.Ser241= (c.723C>T)?

LFNG p.Ser241= (c.723C>T) is associated with spondylocostal dysostosis 3, autosomal recessive (ClinVar).

How common is LFNG p.Ser241= (c.723C>T) in the general population?

LFNG p.Ser241= (c.723C>T) is ultra-rare (popmax 0.0919%, afr) (gnomAD).

LFNG p.Ser241=

c.723C>T · rs115678269 · VCV534226

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0919%, afr)

Conditions

spondylocostal dysostosis 3, autosomal recessive

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.63	donor gain · deltas
Pangolin	Δ0.37	gain · loss 0.03 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP -1.3	GERP -3.1
Overall
CADD	20.4	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0919% African / African-American · 69/75,064 alleles

Filtering AF 0.0744% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0681%

Overall 0.00726% 117/1,612,246 alleles · ultra-rare exomes 72/1,459,862 · genomes 45/152,384 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0919%	1,088
Remaining individualsnot grpmax-eligible	0.0112%	8,919
South Asian	0.0033%	30,336
European (non-Finnish)	0.00305%	32,771
East Asian	0.00223%	44,866
Admixed American	0.00167%	59,952

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: LFNG
Protein: p.Ser241=
Coding: c.723C>T
MANE Select: NM_001040167
dbSNP: rs115678269
Type: single nucleotide variant
Location: chr7:2525555 (GRCh38)
Gene constraint: LOEUF 0.755 · pLI 0.02 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 83.66

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

Disease context

spondylocostal dysostosis 3, autosomal recessive — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

LFNG p.Thr145Met Likely pathogenic ★★ same condition
LFNG c.482-3C>T Uncertain significance ★★ same condition
LFNG p.Ala95Val Uncertain significance ★★ ⚠ same condition
LFNG p.Ala99Thr Uncertain significance ★★ ⚠ same condition
LFNG p.Arg187Cys Uncertain significance ★★ ⚠ same condition
LFNG p.Arg239Trp Uncertain significance ★★ ⚠ same condition
LFNG p.Arg246His Uncertain significance ★★ ⚠ same condition
LFNG p.Arg341Gln 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/lfng-p-ser241 (accessed [today's date]).

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