Is NPHP4 p.Pro831= (c.2493G>A) pathogenic?

NPHP4 p.Pro831= (c.2493G>A) is classified Likely benign in NPHP4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2025-04-28). Very rare (popmax 0.00666%, afr); Associated with nephronophthisis.

What condition is associated with NPHP4 p.Pro831= (c.2493G>A)?

NPHP4 p.Pro831= (c.2493G>A) is associated with nephronophthisis (ClinVar).

How common is NPHP4 p.Pro831= (c.2493G>A) in the general population?

NPHP4 p.Pro831= (c.2493G>A) is very rare (popmax 0.00666%, afr) (gnomAD).

How is Nephronophthisis inherited?

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

NPHP4 p.Pro831=

c.2493G>A · rs546616658 · VCV1093351

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00666%, afr)

Conditions

nephronophthisis

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 -2.9	GERP -3.8
Overall
CADD	3.669	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00666% African / African-American · 5/75,036 alleles

Filtering AF 0.00287% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00195%

Overall 0.0013% 21/1,613,416 alleles · very rare exomes 16/1,461,124 · genomes 5/152,292 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00666%	15,007
South Asian	0.0066%	15,153
East Asian	0.00223%	44,866
Remaining individualsnot grpmax-eligible	0.0016%	62,478
European (non-Finnish)	0.000678%	147,451

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: NPHP4
Protein: p.Pro831=
Coding: c.2493G>A
MANE Select: NM_015102
dbSNP: rs546616658
Type: single nucleotide variant
Location: chr1:5880232 (GRCh38)
Gene constraint: LOEUF 1.183 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.44
Residue 831: the 'sufficient for basal bodies localization' region

Full NPHP4 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

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

For Nephronophthisis (Orphanet):

Inheritance: Autosomal recessive
Onset: Adolescent, Adult, Antenatal, Childhood, Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Finland)

Similar variants

NPHP4 p.Pro831Leu Conflicting classifications of pathogenicity ★ ⚠ same residue
NPHP4 c.2304+1G>A Pathogenic ★★ same condition
NPHP4 c.2611+1G>A Pathogenic/Likely pathogenic ★★ same condition
NPHP4 c.2611+1G>C Pathogenic ★★ same condition
NPHP4 c.3644+1G>A Pathogenic/Likely pathogenic ★★ same condition
NPHP4 c.3644+1G>T Pathogenic/Likely pathogenic ★★ same condition
NPHP4 c.518-2A>G Likely pathogenic ★★ same condition
NPHP4 c.992+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/nphp4-p-pro831 (accessed [today's date]).

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