# NM_138694.4(PKHD1):c.1137C>T (p.Phe379=)

https://sugi.bio/variant/pkhd1-p-phe379

## Summary

**PKHD1 p.Phe379= (c.1137C>T)** is classified **Likely benign** in PKHD1 (ClinVar, Single submitter, 1 submitter; last evaluated 2022-03-15). Absent from gnomAD v4.1; Associated with autosomal recessive polycystic kidney disease.

**At a glance:** Likely benign · review: Single submitter · rsID rs2533402937 · 1 submitter · 1 linked condition · absent from gnomAD v4.1

## For patients & families {#patients}

This is a change in the PKHD1 gene that is classified as likely benign — not considered disease-causing, submitted by 1 submitter, and is linked to autosomal recessive polycystic kidney disease.

*Reference information, not medical advice, and not a prediction for any individual. A genetic counselor or clinician can interpret what it means for you and your family.*

|  |  |
| --- | --- |
| Typical inheritance (of this condition) | Autosomal recessive |
| Age of onset (of this condition) | All ages |
| Prevalence | 1-9 / 100 000 (Germany) |
| Clinical trials | 6 registered for this condition — see ClinicalTrials.gov |
| Diagnostic panels | PKHD1 is a diagnostic-grade gene on 14 Genomics England panels |

**Commonly reported features of Autosomal recessive polycystic kidney disease** (across patients with this condition; presentation varies — frequencies from Orphanet):

- Enlarged kidney — Very frequent (99-80%)
- Polycystic kidney dysplasia — Very frequent (99-80%)
- Hypertension — Very frequent (99-80%)
- Hepatic fibrosis — Very frequent (99-80%)
- Periportal fibrosis — Very frequent (99-80%)
- Renal insufficiency — Frequent (79-30%)
- Cholestasis — Frequent (79-30%)
- Portal hypertension — Frequent (79-30%)

**Support & next steps:** [Condition overview & support (NIH GARD)](https://rarediseases.info.nih.gov/diseases/0008378/index) · [Find a genetic counselor (NSGC)](https://findageneticcounselor.nsgc.org/).

## Identity {#identity}

| Field | Value |
| --- | --- |
| Gene | [PKHD1](https://sugi.bio/atlas/gene/PKHD1/) |
| Protein change (HGVS p.) | p.Phe379= |
| Coding change (HGVS c.) | c.1137C>T |
| MANE Select transcript | [NM_138694](https://www.ncbi.nlm.nih.gov/nuccore/NM_138694) |
| dbSNP | [rs2533402937](https://www.ncbi.nlm.nih.gov/snp/rs2533402937/) |
| Variant type | single nucleotide variant |
| Location | chr6:52060024-52060024 (GRCh38) |
| ClinVar | [VCV2112692](https://www.ncbi.nlm.nih.gov/clinvar/variation/2112692/) |

**All HGVS expressions:** `NC_000006.11:g.51924822G>A`, `NC_000006.12:g.52060024G>A`, `NG_008753.1:g.32602C>T`, `NM_138694.4:c.1137C>T`, `NM_170724.3:c.1137C>T`

## Computational & population evidence {#evidence}

**Concordance:** Mixed / partial computational evidence (see below).

- **Missense predictors (AlphaMissense/REVEL/SaProt) do not apply** to this variant type — they score amino-acid substitutions only. For non-missense variants the computational signal comes from conservation (below), not from a missing predictor score.
- Conservation: phyloP 6.505, GERP 2.04, phastCons 1 — highly conserved position (PP3-type support)
- CADD: **PHRED 9.709**. No single ClinGen-calibrated threshold exists and the expert panels that use CADD disagree — GUCY2D/AIPL1 require ≥ 20.0 for an untranslated-region variant, ABCA4 ≥ 28.1 for a synonymous or indel variant, the Pulmonary Hypertension panel imports Pejaver 2022's missense-calibrated numbers, and the Antibody Deficiencies panel declines CADD entirely for PIK3CD. CADD v1.7 also incorporates Zoonomia phyloP, so it partly re-expresses the conservation above. *Descriptive; no threshold applied.*
- SpliceAI: **no splice effect predicted**. SpliceAI outputs four numbers per variant, not one: acceptor loss, donor loss, acceptor gain, donor gain (DS_AL / DS_DL / DS_AG / DS_DG). A loss score is an existing splice site weakened or destroyed; a gain score is a new site created or an existing one strengthened. The release publishes its own filter rule, which we read from the dataset rather than assume: an allele is reported only if the largest of its four deltas reaches 0.2. No allele at this position is in the release, so all four are under 0.2 for every alternate allele here. No figure is shown because none was read: the bound is deduced from that absence. It is a result, not a gap in our data, because the release scores every possible substitution across the transcripts it covers (Ensembl MANE v1.4) before it filters, so what survives for a gene is one continuous stretch. What is measured is that this position sits inside the stretch covered for PKHD1 (4,414 scored positions, the nearest 5 bases away); what is taken from the release's own description, rather than measured, is that coverage inside that stretch is continuous. On that, SpliceAI did score it. *ClinGen's SVI treats the largest of the four as evidence against a splicing effect at or below 0.1, where it may support BP4, and as uninformative between 0.1 and 0.2. We cannot tell which applies here, so these SpliceAI data support neither BP4 nor PP3; that is a statement about this evidence alone, not about the variant's other evidence.*
- Population frequency: **absent from gnomAD v4.1** — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.

*Computational predictors are not independent (ClinGen Variant Classification guidance): AlphaMissense (Cheng et al. 2023) carries the ACMG weight for missense and conservation (phyloP/GERP/phastCons) for non-missense; REVEL (Pejaver-2022 calibrated strength bands) and SaProt (Su et al. 2023, structure-aware, ClinVar-independent protein language model, raw LLR) are shown as orthogonal agreement signals, not additive. For frequency, the gnomAD v4.1 grpmax filtering allele frequency (FAF95) is ClinGen's designated BA1/BS1 input (gnomAD v4 guidance v3.0, June 2025); BA1/BS1 thresholds are disease-specific, not a blanket 5%. Predictions, not a clinical determination.*

## Gene constraint & dosage {#gene-context}

**PKHD1** population constraint: LOEUF 0.783, pLI 2.8316e-48, missense-Z 1.7677. *Lower LOEUF and higher pLI indicate a gene that tolerates loss-of-function poorly; ClinGen dosage is the curated haploinsufficiency call.*

Curated gene–disease validity (ClinGen):

- **autosomal recessive polycystic kidney disease** — Definitive (AR)

## Protein context {#protein}

Residue **379** lies in the pa14 domain.

## Clinical significance {#significance}

**Likely benign** — review status Single submitter *(criteria provided, single submitter)*, last evaluated 2022-03-15.

**Submitter consensus:** unanimous (1/1 Likely benign).

### Submitter classifications {#submitters}

| Submitter | Classification | Review | Method | Date |
| --- | --- | --- | --- | --- |
| Labcorp Genetics (formerly Invitae), Labcorp | Likely benign | criteria provided, single submitter | clinical testing | 2022-03-15 |

## Associated conditions {#conditions}

[autosomal recessive polycystic kidney disease](https://sugi.bio/atlas/disease/autosomal-recessive-polycystic-kidney-disease/).

**Reported phenotype names (ClinVar):** Autosomal recessive polycystic kidney disease, AR polycystic kidney disease.

## Similar variants {#similar}

Related PKHD1 variant pages (same residue, condition, or type): [PKHD1 c.11174+2T>C](/variant/pkhd1-c-11174-plus-2t-c), [PKHD1 c.11310+1G>C](/variant/pkhd1-c-11310-plus-1g-c), [PKHD1 c.11398+2T>C](/variant/pkhd1-c-11398-plus-2t-c), [PKHD1 c.11507-1G>A](/variant/pkhd1-c-11507-minus-1g-a), [PKHD1 c.11665+1G>A](/variant/pkhd1-c-11665-plus-1g-a), [PKHD1 c.1233+1G>A](/variant/pkhd1-c-1233-plus-1g-a), [PKHD1 c.131-1G>A](/variant/pkhd1-c-131-minus-1g-a), [PKHD1 c.1513-1G>A](/variant/pkhd1-c-1513-minus-1g-a).

### Data sources & attribution {#sources}

ClinVar (NCBI — public domain, built 2026-10-14); gnomAD v4.1 (Broad Institute, built 2026-10-15); AlphaMissense (Cheng et al. 2023, © Google DeepMind — CC BY 4.0, built 2026-01-27); REVEL (Ioannidis et al. 2016 — ODbL, built 2026-07-13); SaProt (Su et al. 2023 — MIT, built 2026-10-14); SpliceAI (Illumina — free for non-commercial use, built 2026-10-13); CADD (Rentzsch et al. 2019, University of Washington — free for non-commercial use, built 2026-10-10); Conservation (phyloP/phastCons/GERP) (UCSC hg38 470-way mammal (Hiller Lab) + Ensembl Compara, built 2026-07-12); gnomAD Non-coding Constraint (Gnocchi) (Chen et al. 2024, Broad Institute — CC0, built 2026-10-11); gnomAD Regional Missense Constraint (Broad Institute — CC0, built 2026-10-13); Pangolin (Zeng & Li 2022 — CC BY 4.0, built 2026-10-11); Repeat regions (UCSC — RepeatMasker, TRF, segmental duplications, built 2026-10-11); ClinGen (ClinGen, built 2026-09-22); UniProt (CC BY 4.0); Reactome / GO (CC BY 4.0, built 2026-09-23); MaveDB (per-record license, built 2026-10-11); CIViC (CC0, built 2026-09-22); Orphanet (Orphanet, built 2026-06-12)

*Primary record: NCBI ClinVar (variation 2112692). Classifications reflect these databases as of the page's build date and may change. Free reference use — not medical advice; consult the primary submitters and a clinician.*