Is CEP164 p.Pro1239= (c.3717G>A) pathogenic?

CEP164 p.Pro1239= (c.3717G>A) is classified Likely benign in CEP164 (ClinVar, Multiple submitters, 4 submitters; last evaluated 2026-01-12). Rare (popmax 0.183%, afr); Associated with nephronophthisis 15.

What condition is associated with CEP164 p.Pro1239= (c.3717G>A)?

CEP164 p.Pro1239= (c.3717G>A) is associated with nephronophthisis 15 (ClinVar).

How common is CEP164 p.Pro1239= (c.3717G>A) in the general population?

CEP164 p.Pro1239= (c.3717G>A) is rare (popmax 0.183%, afr) (gnomAD).

How is Senior-Loken syndrome inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

CEP164 p.Pro1239=

c.3717G>A · rs149567170 · VCV473084

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 4 submitters

gnomAD v4.1

Rare

rare (popmax 0.183%, afr)

Conditions

nephronophthisis 15

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 1.8	GERP -0.77, phastCons 0.99
Overall
CADD	6.509	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.183% African / African-American · 137/75,038 alleles

Filtering AF 0.158% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.148%

Overall 0.0151% 244/1,614,060 alleles · rare

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.183%	548
Middle Eastern	0.0495%	2,020
Remaining individualsnot grpmax-eligible	0.024%	4,167
Admixed American	0.0217%	4,617
European (non-Finnish)	0.00619%	16,164
East Asian	0.00446%	22,433
South Asian	0.0011%	91,068

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: CEP164
Protein: p.Pro1239=
Coding: c.3717G>A
MANE Select: NM_014956
dbSNP: rs149567170
Type: single nucleotide variant
Location: chr11:117408997 (GRCh38)
Gene constraint: LOEUF 1.009 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 63.08 · 4 PDB

Full CEP164 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

nephronophthisis 15 — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Senior-Loken syndrome (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Childhood, Infancy
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

CEP164 p.Pro1239Leu Benign/Likely benign ★★ same residue
CEP164 c.1234-2A>T Likely pathogenic ★★ same condition
CEP164 c.1724+1G>A Likely pathogenic ★★ same condition
CEP164 c.1934+1G>A Likely pathogenic ★★ same condition
CEP164 c.2361+1G>A Likely pathogenic ★★ same condition
CEP164 c.2493+1G>A Likely pathogenic ★★ same condition
CEP164 c.2914-1G>C Likely pathogenic ★★ same condition
CEP164 c.3748+2T>C 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/cep164-p-pro1239 (accessed [today's date]).

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