Is IFT43 p.Ser67= (c.201C>T) pathogenic?

IFT43 p.Ser67= (c.201C>T) is classified Conflicting classifications of pathogenicity in IFT43 (ClinVar, Conflicting submitters, 4 submitters; last evaluated 2026-01-21). Ultra-rare (popmax 0.0989%, afr); Associated with cranioectodermal dysplasia 3.

What condition is associated with IFT43 p.Ser67= (c.201C>T)?

IFT43 p.Ser67= (c.201C>T) is associated with cranioectodermal dysplasia 3, connective tissue disorder, retinitis pigmentosa 81 (ClinVar).

How common is IFT43 p.Ser67= (c.201C>T) in the general population?

IFT43 p.Ser67= (c.201C>T) is ultra-rare (popmax 0.0989%, afr) (gnomAD).

IFT43 p.Ser67=

c.201C>T · rs140127543 · VCV1089443

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

ultra-rare (popmax 0.0989%, afr)

Conditions

cranioectodermal dysplasia 3

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 -1.5	GERP -0.47
Overall
CADD	7.014	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0989% African / African-American · 74/74,802 alleles

Filtering AF 0.0808% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0741%

Overall 0.00541% 87/1,608,940 alleles · ultra-rare exomes 49/1,456,834 · genomes 38/152,106 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.0989%	1,011
Admixed American	0.005%	19,987
Remaining individualsnot grpmax-eligible	0.00321%	31,178
European (non-Finnish)	0.00068%	146,952

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: IFT43
Protein: p.Ser67=
Coding: c.201C>T
MANE Select: NM_001102564
dbSNP: rs140127543
Type: single nucleotide variant
Location: chr14:76022380 (GRCh38)
Gene constraint: LOEUF 1.282 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 64.09 · 3 PDB

Full IFT43 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

cranioectodermal dysplasia 3 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Also linked: connective tissue disorder retinitis pigmentosa 81 short-rib thoracic dysplasia 18 with polydactyly

Similar variants

IFT43 c.148-2A>C Likely pathogenic ★★ same condition
IFT43 c.296-5698C>T Likely pathogenic ★★ same condition
IFT43 c.296-5681A>G Uncertain significance ★★ same condition
IFT43 c.296-5697G>A Uncertain significance ★★ same condition
IFT43 c.444+5G>A Uncertain significance ★★ same condition
IFT43 p.Ala162Val Uncertain significance ★★ ⚠ same condition
IFT43 p.Ala202Val Uncertain significance ★★ ⚠ same condition
IFT43 p.Ala31Pro 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/ift43-p-ser67 (accessed [today's date]).

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