Is NPHP4 p.Thr1225= (c.3675G>A) pathogenic?

NPHP4 p.Thr1225= (c.3675G>A) is classified Likely benign in NPHP4 (ClinVar, Multiple submitters, 2 submitters; last evaluated 2024-08-14). Very rare (popmax 0.00561%, sas); Associated with nephronophthisis.

What condition is associated with NPHP4 p.Thr1225= (c.3675G>A)?

NPHP4 p.Thr1225= (c.3675G>A) is associated with nephronophthisis (ClinVar).

How common is NPHP4 p.Thr1225= (c.3675G>A) in the general population?

NPHP4 p.Thr1225= (c.3675G>A) is very rare (popmax 0.00561%, sas) (gnomAD).

How is Nephronophthisis inherited?

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

NPHP4 p.Thr1225=

c.3675G>A · rs1641090338 · VCV2988496

Likely benign Multiple submitters

Classification

Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

gnomAD v4.1

Rare

very rare (popmax 0.00561%, sas)

Conditions

nephronophthisis

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Pangolin	Δ0.23	gain · loss 0.14 · SpliceAI below 0.2 · independent
Constraint at this position
Conservation	phyloP -6	GERP -3.6
Overall
CADD	1.017	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00561% South Asian · 5/89,140 alleles

Filtering AF 0.00214% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.00139%

Overall 0.000946% 15/1,586,354 alleles · very rare exomes 14/1,434,154 · genomes 1/152,200 · joint denominator

Ancestry group	Frequency	1 in
South Asiangrpmax	0.00561%	17,828
African / African-American	0.00403%	24,815
European (non-Finnish)	0.000603%	165,856

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.Thr1225=
Coding: c.3675G>A
MANE Select: NM_015102
dbSNP: rs1641090338
Type: single nucleotide variant
Location: chr1:5865243 (GRCh38)
Gene constraint: LOEUF 1.183 · pLI <0.01 (gnomAD)
Structure: AlphaFold pLDDT 72.44
Residue 1225: the 'sufficient for basal bodies localization' region; a UniProt-annotated variant site (in slsn4; benign)

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.Thr1225Met Benign/Likely benign ★★ 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-thr1225 (accessed [today's date]).

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